USPTO Patents Application 10551504

WORLD INTELLECTUAL PROPERTY ORGANIZATION

International Bureau

PCT

INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT)

(51) International Patent Classification 5 •

C12N 15/13, C07K 15/28, C12N 15/62,
A61K 39/395

Al

(11) International Publication Number:
(43) International Publication Date:

WO 94/13806

23 June 1994 (23.06.94)

(21) International Application Number:

PCT/US93/12039

(22) International Filing Date: 10 December 1993 (10.12.93)

(30) Priority Data:

07/990,263

1 1 December 1992 (1 1 .12.92) US

(71) Applicant: THE DOW CHEMICAL COMPANY [US/US];

2030 Dow Center, Abbott Road, Midland, MI 48640 (US).

(72) Inventors: MEZES, Peter, S.; 25 Sill Lane, Oldlyme, CT 06371

(US). GOURDE, Brian, B.; 3713 Orchard Drive, Midland,
MI 48640 (US).

(74) Agent: ULMER, Duane, C; The Dow Chemical Company,
Patent Department, P.O. Box 1967, Midland, MI 48641-
1967 (US).

(81) Designated States: AU, CA, JP, European patent (AT, BE,
CH, DE, DK, ES, FR, GB, GR, IE, IT, LU, MC, NL, FT,
SE).

Published

With international search report.

Before the expiration of the time limit for amending the
claims and to be republished in the event of the receipt of
amendments.

(54) Title: MULTIVALENT SINGLE CHAIN ANTIBODIES

(57) Abstract

The present invention discloses
multivalent single chain antibodies
which have two or more biologically
active antigen binding sites. The
multivalent single chain antibodies
are formed by using a peptide linker
to covalently link two or more single
chain antibodies, each single chain
antibody having a variable light domain
linked to a variable heavy chain domain
by a peptide linker.

Schematic Representation Of Covalently &
Non-Covalently Linked Single Chain Fv Multimers

L — L — L — COOH

scFv2 (LHLH)

V L V„ V H V l

HOOC

^ — ^ 'COOH

SCFv2 (LHHL)

COOH

Fv2

FOR THE PURPOSES OF INFORMATION ONLY

Codes used to identify States party to the PCT on die front pages of pamphlets publishing international
applications under the PCT.

AT

Austria

GB

United Kingdom

MR

Mauritania

AU

Australia

GE

Georgia

MW

Malawi

BB

Barbados

GN

Guinea

NE

Niger

BE

Belgium

GR

Greece

NL

Netherlands

BF

Burkina Faso

HU

Hungary

NO

Norway

BG

Bulgaria

IE

Ireland

NZ

New Zealand

BJ

Benin

IT

Italy

PL

Poland

BR

Brazil

JP

Japan

PT

Portugal

BY

Belarus

KE

Kenya

RO

Romania

CA

Canada

KG

Kyrgystan

RU

Russian Federation

CF

Central African Republic

KP

Democratic People's Republic

SD

Sudan

CG

Congo

of Korea

SE

Sweden

CH

Switzerland

KR

Republic of Korea

SI

Slovenia

CI

C6te d'lvoire

KZ

Kazakhstan

SK

Slovakia

CM

Cameroon

U

Liechtenstein

SN

Senegal

CN

China

LK

Sri Lanka

TD

Chad

cs

Czechoslovakia

LU

Luxembourg

TG

Togo

cz

Czech Republic

LV

Latvia

TJ

Tajikistan

DE

Germany

MC

Monaco

TT

Trinidad and Tobago

DK

Denmark

MD

Republic of Moldova

UA

Ukraine

ES

Spain

MG

Madagascar

US

United States of America

FI

Finland

ML

Mali

uz

Uzbekistan

FR

France

MN

Mongolia

VN

Viet Nam

GA

Gabon

WO 94/13806

PCT/US93/12039

MULTIVALENT SINGLE CHAIN ANTIBODIES

The present invention relates to single chain multivalent antibodies.

Antibodies are proteins belonging to a group of immunoglobulins elicited by the
5 immune system in response to a specific antigen or substance which the body deems foreign.
There are five classes of human antibodies, each class having the same basic structure. The
basic structure of an antibody is a tetramer, or a multiple thereof, composed of two identical
heterodimers each consisting of a light and a heavy chain. The light chain is composed of one
variable (V) and one constant (Q domain, while a heavy chain is composed of one variable and
10 three or more constant domains. The variable domains from both the light and heavy chain,
designated V L and V H respectively, determine the specificity of an immunoglobulin, while the
constant (C) domains carry out various effector functions.

Amino acid sequence data indicate that each variable domain comprises three
complementarity determining regions (CDR) flanked by four relatively conserved framework
15 regions (FR). The FR are thought to maintain the structural integrity of the variable region
domain. The CDR have been assumed to be responsible for the binding specificity of individual
antibodies and to account for the diversity of binding of antibodies.

As the basic structure of an antibody contains two heterodimers, antibodies are
multivalent molecules. For example, the IgG classes have two identical antigen binding sites,
20 while the pentameric IgM class has 10 identical binding sites.

Monoclonal antibodies having identical genetic parentage and binding specificity
have been useful both as diagnostic and therapeutic agents. Monoclonal antibodies are
routinely produced by hybridomas generated by fusion of mouse lymphoid cells with an
appropriate mouse myeloma cell line according to established procedures. The administration
25 of murine antibodies for in vivo therapy and diagnostics in humans is limited however, due to
the human anti-mouse antibody response illicited by the human immune system.

Chimeric antibodies, in which the binding or variable regions of antibodies
derived from one species are combined with the constant regions of antibodies derived from a
different species, have been produced by recombinant DNA methodology. See, for example,
30 Sahagenetal.,7. Immunol., 137:1066-1074(1986); Sun etal.,Proc. Natl. Acad. Sci. USA,

82:214-218 (1987); Nishimura et al.. Cancer Res., 47:999-1005 (1987); and Lie et al. Proc Natl.
Acad. Sci. USA, 84:3439-3443 (1987) which disclose chimeric antibodies to tumor-associated
antigens. Typically, the variable region of a murine antibody is joined with the constant region
of a human antibody. It is expected that as such chimeric antibodies are largely human in
35 composition, they will be substantially less immunogenic than murine antibodies.

Chimeric antibodies still carry the Fc regions which are not necessary for antigen
binding, but constitute a major portion of the overall antibody structure which affects its
pharmacokinetics. For the use of antibodies in immunotherapy or immunodiagnostics, is it

WO 94/13806

PCT/US93/12039

desirable to have antibody-l ike molecules which localize and bind to the target tissue rapidly
and for the unbound material to quickly clear from the body. Generally, smaller antibody
fragments have greater capillary permeability and are more rapidly cleared from the body
than whole antibodies.

- Since it is the variable regions of light and heavy chains that interact with an

antigen, single chain antibody fragments (scFvs) have been created with one V L and one V H ,
containing all six CDR's, joined by a peptide linker (U.S. Patent 4,946,778) to create a V L -L-V H
polypeptide, wherein the L stands for the peptide linker. A scFv wherein the V L and V H
domains are orientated V H -L-V L is disclosed in U.S. Patent 5,132,405.

10 As the scFvs have one binding site as compared to the minimum of two for

complete antibodies, the scFvs have reduced avidity as compared to the antibody containing

two or more binding sites.

It would therefore be advantageous to obtain constructions of scFvs having more
than one binding site to enhance the avidity of the polypeptide, and retain or increase their

1 5 antigen recognition properties. In addition, it would be beneficial to obtain multivalent scFvs
which are bispecif ic to allow for recognition of different epitopes on the target tissue, to allow
for antibody-based recruitment of other immune effector functions, or allow antibody capture
of a therapeutic or diagnostic moiety.

It has been found that single chain antibody fragments, each having one V H and

20 one V L domain covalently linked by a first peptide linker, can be covalently linked by a second
peptide linker to forma multivalent single chain antibody which maintains the binding affinity
of a whole antibody. In one embodiment, the present invention is a multivalent single chain
antibody having affinity for an antigen wherein the multivalent single chain antibody
comprises two or more light chain variable domains and two or more heavy chain variable

25 domains; wherein, each variable domain is linked to at least one other variable domain.

in another embodiment, the present invention is a multivalent single chain antibody
which comprises two or more single chain antibody fragments, each fragment having affinity
for an antigen wherein the fragments are covalently linked by a first peptide linker and each
fragment comprising:

3Q (a) a first polypeptide comprising a light chain variable domain;

(b) a second polypeptide comprising a heavy chain variable domain; and

(c) a second peptide linker linking the first and second polypeptides into a functional
binding moiety.

In another embodiment, the invention provides a DNA sequence which codes for
35 a multivalent single chain antibody, the multivalent single chain antibody comprising two or
more single chain antibody fragments, each fragment having affinity for an antigen wherein
the fragments are covalently linked by a first peptide linker and each fragment comprising:
(a) a first polypeptide comprising a light chain variable domain;

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PCT/US93/12039

(b) a second polypeptide comprising a heavy chain variable domain; and

(c) a second peptide linker linking the first and second polypeptides into a functional
binding moiety.

The multivalent single chain antibodies allow for the construction of an antibody
5 fragment which has the specificity and avidity of a whole antibody but are smaller in size

allowing for more rapid capillary permeability. Multivalent single chain antibodies also allow
for the construction of a multivalent single chain antibody wherein the binding sites can be
two different antigenic determinants.
BRIEF DESCRIPTION OF THE DRAWINGS
1 o Figure 1 illustrates covalently linked single chain antibodies having the

configuration V L -L-V H -L-V L -L-V H (LHLH) and V L -L-V H -L-V H -L-V U (LHHL) and a noncovalently
linked Fv single chain antibody (Fv2).

Figure 2 illustrates the nucleotide sequence of CC49 V L .
Figure 3 illustrates the amino acid sequence of CC49 V L .
1 5 Figure 4 illustrates the nucleotide sequence of CC49 V H .

Figure 5 illustrates the amino acid sequence of CC49 Vh-

Figure 6 illustrates the nucleotide sequence and amino acid sequence of the CC49
single chain antibody LHLH in p49LHLH.

Figure 7 illustrates the nucleotide sequence and amino acid sequence of the CC49
20 single antibody LHHL in p49LHHL.

Figure 8 illustrates construction of plasmids pSL301 Tand pSL301 HT.
Figure 9 illustrates construction of plasmid p49LHHL.
Figure 10 illustrates construction of plasmid p49LHLH.

Figure 1 1 illustrates the results of a competition assay using CC49 IgG, CC49 scFv2,
25 and CC49 scFv using biotinyiated CC49 IgG as competitor.

The entire teaching of ail references cited herein are hereby incorporated by

reference.

Nucleic acids, amino acids, peptides, protective groups, active groups and such,
when abbreviated, are abbreviated according to the IUPAC IUB (Commission on Biological
30 Nomenclature) or the practice in the fields concerned.

The term "single chain antibody fragment" (scFv) or "antibody fragment" as used
herein means a polypeptide containing a v\ domain linked to a V H domain by a peptide linker
(L), represented by V[_-L-Vh- The order of the V L and V H domains can be reversed to obtain
polypeptides represented as V H -L-V L . "Detain" is a segment of protein that assumes a discrete
35 function, such as antigen binding or antigen recognition.

A "multivalent single chain antibody" means two or more single chain antibody
fragments covalently linked by a peptide linker. The antibody fragments can be joined to form
bivalent single chain antibodies having the order of the V L and V H domains as follows:

WO 94/13806

PCT/US93/12039

V L -L-V H -L-V L -L-V H; V L -L-V H -L-V H -L-V L ; V H -L-V L -L-V H -L-V L ; or V H -L-V L -L-V L -L-V H .
Single chain multivalent antibodies which are trivalent and greater have one or more antibody
fragments joined to a bivalent single chain antibody by an additional interpeptide linker. In a
preferred embodiment, the number of V L and V H domains is equivalent.

5 The present invention also provides for multivalent single chain antibodies which

can be designated V H -L-V H -L-V L -L-V L or V L -L-V L -l-V H -L-V H .

Covalently linked single chain antibodies having the configuration V L -L-V H -L-\/ L -L-
-V H (LHLH) and V L -L-V H -L-V H -L-V L (LHHL) are illustrated in Figure 1. A noncovalently linked Fv
single chain antibody (Fv2) is also illustrated in Figure 1 .

10 The single chain antibody fragments for use in the present invention can be

derived from the light and/or heavy chain variable domains of any antibody. Preferably, the
light and heavy chain variable domains are specific for the same antigen. The individual
antibody fragments which are joined to form a multivalent single chain antibody may be
directed against the same antigen or can be directed against different antigens.

1 5 To prepare a vector containing the DNA sequence for a single chain multivalent

antibody, a source of the genes encoding for these regions is required. The appropriate DNA
sequence can be obtained from published sources or can be obtained by standard procedures
known in the art. For example, Kabat et at. f Sequences of Proteins of Immunological Interest
4t/>ed.t (1991), published by The U.S. Department of Health and Human Services, discloses

20 sequences of most of the antibody variable regions which have been described to date.

When the genetic sequence is unknown, it is generally possible to utilize cDNA
sequences obtained from mRNA by reverse transcriptase mediated synthesis as a source of DNA
to clone into a vector. For antibodies, the source of mRNA can be obtained from a wide range
of hybridomas. See, for example, the catalogue ATCC Cell Lines and Hybridomas, American

25 Type Culture Collection, 20309 Parklawn Drive, Rockville Md., USA (1990). Hybridomas

secreting monoclonal antibodies reactive with a wide variety of antigens are listed therein, are
available from the collection, and usable in the present invention. These cell lines and others of
similar nature can be utilized as a source of mRNA coding for the variable domains or to obtain
antibody protein to determine amino acid sequence of the monoclonal antibody itself.

30 Variable regions of antibodies can also be derived by immunizing an appropriate

vertebrate, normally a domestic animal, and most conveniently a mouse. The immunogen will
be the antigen of interest, or where a hapten, an antigenic conjugate of the hapten to an
antigen such as keyhole limpet hemocyanin (KLH). The immunization may be carried out
conventionally with one or more repeated injections of the immunogen into the host mammal,

35 normally at two to three week intervals. Usually, three days after the last challenge, the spleen
is removed and dissociated into single cells to be used for cell fusion to provide hybridomas
from which mRNA can readily be obtained by standard procedures known in the art.

WO 94/13806

PCT/US93/12039

When an antibody of interest is obtained, and only its amino acid sequence is
known, it is possible to reverse translate the sequence.

The V L and Vh domains for use in the present invention are preferably obtained
from one of a series of CC antibodies against tumor-associated glycoprotein 72 antigen

5 (TAG-72) disclosed in published PCT Application WO 90/04410 on May 3, 1990, and published
PCT Application WO 89/00692 on January 26, 1989. More preferred are the V L and V H domains
from the monoclonal antibody designated CC49 in PCT Publications WO 90/04410 and
WO 89/00692. The nucleotide sequence (SEQ ID NO: 1) which codes for the V L of CC49 is
substantially the same as that given in Figure 1. The amino acid sequence (SEQ ID NO: 2) of the

10 V L of CC49 is substantially the same as that given in Figure 2. The nucleotide sequence (SEQ ID
NO: 3) which codes for the V H of CC49 is substantially the same as that given in Figure 3. The
amino acid sequence (SEQ ID NO: 4) for the V H of CC49 is substantially the same as that given in
Figure 4.

To form the antibody fragments and multivalent single chain antibodies of the

1 5 present invention, it is necessary to have a suitable peptide linker. Suitable linkers for joining
the V H and domains are those which allow the Vh and V L domains to fold into a single
polypeptide chain which will have a three dimensional structure very similar to the original
structure of a whole antibody and thus maintain the binding specificity of the whole antibody
from which antibody fragment is derived. Suitable linkers for linking the scFvs are those which

20 allow the linking of two or more scFvs such that the V H and V L domains of each

immunoglobulin fragment have a three dimensional structure such that each fragment
maintains the binding specificity of the whole antibody from which the immunoglobulin
fragment is derived. Linkers having the desired properties can be obtained by the method
disclosed in U.S. Patent 4,946,778, the disclosure of which is hereby incorporated by reference.

25 From the polypeptide sequences generated by the methods described in the 4,946,778, genetic
sequences coding for the polypeptide can be obtained.

Preferably, the peptide linker joining the V H and V L domains to form a scFvand
the peptide linker joining two or more scFvs to form a multivalent single chain antibody have
substantially the same amino acid sequence.

30 It is also necessary that the linker peptides be attached to the antibody fragments

such that the binding of the linker to the individual antibody fragments does not interfere with
the binding capacity of the antigen recognition site.

A preferred linker is based on the helical linker designated 205C as disclosed in
Pantolianoet al. Biochem., 30, 101 17-10125 (1991) but with the first and last amino acids

35 changed because of the codon dictated by the Xho I site atone end and the Hind III site at the
other. The amino acid sequence (SEQ ID NO: 5) of the preferred linker is as follows:

Leu-Ser-AI a-Asp-Asp- Al a- Lys- Lys- Asp-AI a-Al a- Lys-Lys-Asp-Asp- Al a-Lys- Ly s- Asp- Asp- Al a-
-Lys-Lys-A;-:* ,„eu.

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PCT/US93/12039

The linker is generally 10 to 50 amino acid residues. Preferably, the linker is 10 to
30 amino acid residues. More preferably the linker is 12 to 30 amino acid residues. Most
preferred is a linker of 1 5 to 25 amino acid residues.

Expression vehicles for production of the molecules of the invention include

5 plasmids or other vectors. In general, such vectors contain replicon and control sequences
which are derived from species compatible with a host cell. The vector ordinarily carries a
replicon site, as well as specific genes which are capable of providing phenotypic selection in
transformed cells. For example, E. coli is readily transformed using pBR322 [Bolivar et al.. Gene,
2, 95- (1977), orSambrook et al., Molecular Cloning, Cold Spring Harbor Press, New York, 2nd

10 Ed. (1989)].

Plasmids suitable for eukaryotic cells may also be used. S. cerevisiae, or common
baker's yeast, is the most commonly used among eukaryotic microorganisms, although a
number of other strains, such as Pichia pastoris, are available. Cultures of cells derived from
multicellular organisms such as SP2/0 or Chinese Hamster Ovary (CHO), which are available from

1 5 the ATCC, may also be used as hosts. Typical of vector plasmids suitable for mammalian cells
are pSV2neo and pSV2gpt (ATCC); pSVL and pKSV-1 0 (Pharmacia), pBPV-1/pML2d
(International Biotechnology, Inc.).

The use of prokaryotic and eukaryotic viral expression vectors to express the
genes for polypeptides of the present invention is also contemplated.

20 It is preferred that the expression vectors and the inserts which code for the single

chain multivalent antibodies have compatible restriction sites at the insertion junctions and
that those restriction sites are unique to the areas of insertion. Both vector and insert are
treated with restriction endonucleases and then ligated by any of a variety of methods such as
those described in Sambrook et al., supra.

25 Preferred genetic constructions of vectors for production of single chai n

multivalent antibodies of the present invention are those which contain a constitutively active
transcriptional promoter, a region encoding signal peptide which will direct synthesis/secretion
of the nascent single chain polypeptide out of the cell. Preferably, the expression rate is
commensurate with the transport, folding and assembly steps to avoid accumulation of the

30 polypeptide as insoluble material. In addition to the replicon and control sequences,

additional elements may also be needed for optimal synthesis of single chain polypeptide.
These elementsmay include splice signals, as well as transcription promoter, enhancers, and
termination signals. Furthermore, additional genes and their products may be required to
facilitate assembly and folding (chaperones).

35 Vectors which are commercially available can easily be altered to meet the above

criteria for a vector. Such alterations are easily performed by those of ordinary skill in the art in
light of the available literature and the teachings herein.

WO 94/13806

PCT/US93/12039

Additionally, it is preferred that the cloning vector contain a selectable marker,
such as a drug resistance marker or other marker which causes expression of a selectable trait
by the host cell. "Host cell" refers to cells which can be recombinantly transformed with vectors
constructed using recombinant D IMA techniques. A drug resistance or other selectable marker

5 is intended in part to facilitate in the selection of transformants. Additionally, the presence of
a selectable marker, such as a drug resistance marker, may be of use in keeping contaminating
microorganisms from multiplying in the culture medium. In this embodiment, such a pure
culture of the transformed host cell would be obtained by culturingthe cells under conditions
which require the induced phenotypefor survival.

to Recovery and purification of the present invention can be accomplished using

standard techniques known in the art. For example, if they are secreted into the culture
medium, the single chain multivalent antibodies can be concentrated by ultrafiltration. When
the polypeptides are transported to the periplasmic space of a host cell, purification can be
accomplished by osmotically shocking the cells, and proceeding with ultrafiltration, antigen

^ 5 affinity column chromatography or column chromatography using ion exchange

chromatography and gel filtration. Polypeptides which are insoluble and present as refractile
bodies, also called inclusion bodies, can be purified by lysis of the cells, repeated centrifugation
and washing to isolate the inclusion bodies, solubilization, such as with guanidine-HCI, and
refolding followed by purification of the biologically active molecules.

20 The activity of single chain multivalent antibodiescan be measured by standard

assays known in the art, for example competition assays, enzyme-linked immunosorbant assay
(ELISA), and radioimmunoassay (RIA).

The multivalent single chain antibodies of the present invention provide unique
benefits for use in diagnostics and therapeutics. The use of multivalent single chain antibodies

25 afford a number of advantages over the use of larger fragments or entire antibody molecules.
They reach their target tissue more rapidly, and are cleared more quickly from the body.

For diagnostic and/or therapeutic uses, the multivalent single chain antibodies
can be constructed such that one or more antibody fragments are directed against a target
tissue and one or more antibody fragments are directed against a diagnostic or therapeutic

30 agent.

The invention also concerns pharmaceutical compositions which are particularly
advantageous for use in the diagnosis and/or therapy of diseases, such as cancer, where target
antigens are often expressed on the surface of cells. For diagnostic and/or therapeutic uses, the
multivalent single chain antibodies can be conjugated with an appropriate imaging or
35 therapeutic agent by methods known in the art. The pharmaceutical compositions of the
invention are prepared by methods known in the art, e.g., by conventional mixing, dissolving
or lyophilizing processes.

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PCT/US93/12039

The invention will be further clarified by a consideration of the following
examples, which are intended to be purely exemplary of the present invention.

5

10

15

20

25

35

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ABBREVIATIONS

10

15

20

25

30

BCIP
bp

Bis-Tris
propane

BSA

CDR

ELISA

Fv2

IEF

Kbp

LB

Mab

MES

MW

NBT

Oligo

PAG

PAGE

PBS

PCR

pSCFV

RIGS

RIT

SCFv

SCFv2

SDS
TBS
Tris
TTBS

V H

5-bromo-4-chloro-3-indoyl phosphate
base pair

( 1, 3-bis [ tris (hydroxymethyl ) -me thy lam i no] -
propane)

bovine serum albumin
Complementarity determining region
enzyme linked immunosorbent assay
non-covalent single chain Fv dimer
isoelectric focusing
kilo base pair
Lur ia-Bertani medium
monoclonal antibody

2-<N-Morpholino)ethane sulfonic acid

molecular weight

nitro blue tetrazolium chloride

Oligonucleotides

polyacrylamide gel

polyacrylamide gel electrophoresis

phosphate buffered saline

polymerase chain reaction

plasmid containing DNA sequence coding for SCFV
radio immunoguided surgery
radio immunotherapy

single chain Fv immunoglobulin fragment monomer

single chain Fv immunoglobulin fragment dimer
covalently linked

sodium dodecyl sulfate

Tr is-buf f ered saline

(Tris [hydroxymethyl] ami nome thane )

Tween-20 wash solution

immunoglobulin heavy chain variable domain
immunoglobulin light chain variable domain

35

-9-

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Antibodies

CC49: A murine monoclonal antibody specific to the human tumor-associated
glycoprotein 72 (TAG-72) deposited as ATCC No. HB9459.

CC49FAB : An antigen binding portion of CC49 consisting of an intact light chain
5 linked to the N-terminal portion of the heavy chain.

CC49 scFv : Single chain antibody fragment consisting of two variable domains of
CC49 antibody joined by a peptide linker.

CC49 Fv2 : Two CC49 scFv non-covalently linked to form a dimer. The number
after Fv refers to the number of monomer subunits of a given molecule, e.g., CC49 Fv6 refers to
1 o the hexamer multimers.

CC49 scFv2 : Covalently-linked single chain antibody fragment consisting of two
CC49 V L domains and two V H domains joined by three linkers. Six possible combinations for the
order of linking the V L (L) and the V H (H) domains together are: LHLH, LHHL f LLHH, HLLH, HLHL,
and HHLL
15 Plasmids

pSCFV UHM : Plasmid containing coding sequence for scFv consisting of a CC49
variable light chain and a CC49 variable heavy chain joined by a 25 amino acid linker.

P49LHLH or p49LHHL : Plasmids containing the coding sequence for producing
CC49 scFv2 LHLH or LHHL products, respectively.
20 EXAMPLES

General Experimental

Procedures for molecular cloning are as those described in Sambrook et al. f
Molecular Cloning, Cold Spring Harbor Press, New York, 2nd Ed. (1989) and Ausubel et al.,
Current Protocols in Molecular Biology, John Wiley and Sons, New York (1 992), the disclosures
25 of which are hereby incorporated by reference.

All water used throughout was deionized distilled water.
Oligonucleotide Synthesis and Purification

All oligonuclotides (oligos) were synthesized on either a Model 380A or a
Model 391 DNA Synthesizer from Applied Biosystems (Foster City, CA) using standard
30 P-cyanoethyl phosphoramidites and synthesis columns. Protecting groups on the product were
removed by heating in concentrated ammonium hydroxide at 55°C for 6 to 1 5 hours. The
ammonium hydroxide was removed through evaporation and the crude mixtures were
resuspended in 30 to 40 ul of sterile water. After electrophoresis on polyacrylamide-urea gels,
the oligos were visualized using short wavelength ultraviolet (UV) light. DNA bands were
35 excised from the gel andeluted into 1 mLof 100 mMTris-HCI, pH 7.4, 500 mM NaCI, 5 mM EDTA
over 2 hours at 65°C. Final purification was achieved by applying the DNA to Sep-Pac™ C-18
columns (Millipore, Bedford, MA) and eluting the bound oligos with 60 percent methanol. The

-10-

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■

PCT/US93/12039

solution volume was reduced to approximately 50 \xL and the DNA concentration was
determined by measuring the optical density at 260 nm (OD ).

260

Restriction Enzyme Digests

All restriction enzyme digests were performed using Bethesda Research

5 Laboratories (Gaithersburg, MD), New England Biolabs, Inc. (Beverly, MA) or Boehringer
Mannheim (BM, Indianapolis, IN) enzymes and buffers following the manufacturer's
recommended procedures. Digested products were separated by polyacrylamide gel
electrophoresis (PAGE). The gels were stained with ethidium bromide, the DNA bands were
visualized using long wavelength UV light and the DNA bands were then excised. The gel slices

10 were placed In dialysis tubing (Union Carbide Corp., Chicago) containing 5 mM Tris, 2.5 mM
acetic acid, 1 mM EDTA, pH 8.0 and eluted using a Max Submarine electrophoresis apparatus
(Hoefer Scientific Instruments, CA). Sample volumes were reduced on a Speed Vac
Concentrator (Savant Instruments, Inc., NY). The DNA was ethanol precipitated and redissolved
in sterile water.

15 Enzyme Linked Immunosorbent Assay (ELISA)

TAG-72 antigen, prepared substantially as described by Johnson et al, Can. fles.,
46, 850-857 (1986), was adsorbed onto the wells of a polyvinyl chloride 96 well microtiter plate
(Dynatech Laboratories, Inc., Chantiily, VA) by drying overnight. The plate was blocked with
1 percent BSA in PBS for 1 hour at 31°C and then washed 3 times with 200 jiL of PBS,

20 0.05 percent Tween-20. 25 pL of test antibodies and 25 of biotinylated CC49 (1/20,000

dilution of a 1 mg/mL solution) were added to the wells and the plate incubated for 30 minutes
at31°C The relative amounts of TAG-72 bound to the plate, biotinylated CC49, streptavidin-
alkaline phosphatase, and color development times were determined empirically in order not
to have excess of either antigen or biotinylated CC49, yet have enough signal to detect

25 competition byscFv. Positive controls were CC49 at 5 pg/mL and CC49Fabat 10jig/mL.

Negative controls were 1 percent BSA in PBS and/or concentrated LB. Unbound proteins were
washed away. 50 pL of a 1 : 1 000 dilution of streptavidin conjugated with alkaline phosphatase
(Southern Biotechnology Associates, Inc., Birmingham, AL) were added and the plate was
incubated for 30 minutes at 31°C. The plate was washed 3 more times. 50pLof a

30 para-nitrophenyl-phosphate solution (Kirkegaard & Perry Laboratories, Inc., Gaithersburg, MD)
were added and the color reaction was allowed to develop for a minimum of 20 minutes. The
relative amount of scFv2 binding was measured by optical density scanning at 404-450 nm
using a microplate reader (Molecular Devices Corporation, Manlo Park, CA). Binding of the
scFv2 species resulted in decreased binding of the biotinylated CC49 with a concomitant

35 decrease in color development
SDS-PAGE and Western Blotting

Samples for SDS-PAGE analysis (20 jiL) we*e orepared by boiling in a non-reducing
sample preparation buffer-Seprasol I (Integrated Separation Systems (ISS), Natick, MA) for

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5 minutes and foaded on 10-20 percent gradient poiyacrylamide Daiichi Minigeis as per the
manufacturer's directions (ISS).

Electrophoresis was conducted using a Mini 2-gel apparatus (ISS) at 55 mA per gel
at constant current for approximately 75 minutes. Gels were stained inCoomassie Brilliant Blue

5 R-250(Bio-Rad, Richmond, CA) for at least 1 hour and destained. Molecular weight standards
were prestained (Mid Range Kit, Diversified Biotech, Newton Center, MA) and included the
following proteins: Phosphorylase b, glutamate dehydrogenase, ovalbumin, lactate
dehydrogenase, carbonic amhydrase, B-lactoglobulin and cytochrome C The corresponding
MWsare: 95,500, 55,000, 43,000, 36,000, 29,000, 18,400, and 12,400, respectively.

1 0 When Western analyses were conducted, a duplicate gel was also run. After

electrophoresis, one of the gels was equilibrated for 15-20 minutes in anode buffer #1 (0.3 M
Tris-HCI pH 10.4). An Immobilon-P PVDF (polyvinylidene dichlorine) membrane (Millipore,
Bedford, MA) was treated with methanol for 2 seconds, and immersed in water for 2 minutes.
The membrane was then equilibrated in anode buffer #1 for 3 minutes. A Milliblot-SDE

1 5 apparatus (Millipore) was utilized to transfer proteins in the gel to the membrane. A drop of
anode buffer #1 was placed in the middle ofthe anode electrode surface. A sheet of Whatman
3MM filter paper was soaked in anode buffer #1 and smoothly placed on the electrode surface.
Another filter paper soaked in anode buffer #2 (25 mM tris pH 10.4) was placed on top ofthe
first one. A sandwich was made by next adding the wetted PVDF membrane, placing the

20 equilibrated gel on top of this and finally adding a sheet of filter paper soaked in cathode
buffer (25mM Tris-HCI, pH 9.4 in 40 mM glycine). Transfer was accomplished in 30 minutes
using 250 mA constant current (initial voltage ranged from 8-20 volts).

After blotting, the membrane was rinsed briefly in water and placed in a dish
with 20 ml blocking solution (1 percent bovine serum albumin (BSA) (Sigma, St. Louis, MO) in

25 Tris-buffered saline (TBS)). TBS was purchased from Pierce Chemical (Rockford, IL) as a

preweighed powder such that when 500 mL water is added, the mixture gives a 25 mM Tris,
0.15 M sodium chloride solution at pH 7.6. The membranes were blocked for a minimum of

1 hour at ambient temperature and then washed 3 times for 5 minutes each using 20 mL

0.5 percent Tween-20 wash solution (TTBS). To prepare the TTBS, 0.5mL of Tween 20 (Sigma)
30 was mixed per liter of TBS. The probe antibody used was 20 mL biotinylated FAID1 4 solution
(10 jig per 20 mL antibody buffer). Antibody buffer was made by adding 1 g BSA per 100 mLof
TTBS. After probing for 30-60 minutes at ambient temperature, the membrane was washed
3 times with TTBS, as above.

Next, the membrane was incubated for 30-60 minutes at ambient temperature
35 with 20 mL of a 1 :500 dilution in antibody buffer of streptavidin conjugated with alkaline
phosphatase (Southern Biotechnology Associates, Birmingham, AL). The wash step was again
repeated after this, as above. Prior to the color reaction, membranes were washed for

2 minutes in an alkaline carbonate buffer (20 mL). This buffer is 0.1 M sodium bicarbonate,

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1 mM MgCl 2 -H 2 0, pH 9.8. To make up the substrate for alkaline phosphatase, nitroblue
tetrazolium (NBT) chloride (50 mg, Sigma) was dissolved in 70 percent dimethylformamide.
5-Bromo-4-chloro-3-indoyl phosphate (BGP) (25 mg, Sigma) was separately dissolved in
100 percent dimethylformamide. 5-Bromo-4-chloro-3-indoy! phosphate (BCIP) 25 mg, Sigma)
5 was separately dissolved in 100 percent dimethylformamide. These solutions are also
commercially available as a Western developing agent sold by Promega. For color
development, 120 pL of each were added to the alkaline solution above and allowed to react
for 15 minutes before they were washed from the developed membranes with water.
Biotinvlated FAID14

1 0 FAID14 is a murine anti-idiotypic antibody (lgG2a, K isotype) deposited as ATCC

No. CRL 10256 directed against CC49. FAID14 was purified using a Nygene Protein A affinity
column (Yonkers, NY). The manufacturer's protocol was followed, except that 0.1 M sodium
citrate, pH 3.0 was used as the elution buffer. Fractions were neutralized to pH ~7 using 1.0 M
Tris-HCI pH 9.0. The biotinylation reaction was set up as follows. FAID14(1 mg, 100pLin

15 water) was mixed with 100pLof 0.1 M Na 2 C0 3 pH9.6. Biotinyl-e-amino-caproic acid N-hydroxy
succinimide ester (Biotin-X-NHS) (Calbiochem, LaJolla, CA) (2.5 mg) was dissolved in 0.5 mL
dimethylsulfoxide. Biotin-X-NHS solution (20 \lL) was added to the FAID14 solution and
allowed to react at 22°C for 4 hours. Excess biotin and impurities were removed by gel
filtration, using a Pharmacia Superose 12 HR10/30 column (Piscataway, NJ). At a flow rate of

20 0.8mL/min, the biotinylated FAID14 emerged with a peak at 16.8min. The fractions making up
this peak were pooled and stored at 4°C and used to detect the CC49 idiotype as determined by
the CC49 V, and V u CDRs.

L H

Isoelectric Focusing (IEF)

Isoelectric points (pi's) were predicted using a computer program called PROTEIN-

25 -TITRATE, available through DNASTAR (Madison, Wl). Based on amino acid composition with
an input sequence, a MW value is given, in addition to the pi. Since Cys residues contribute to
the charge, the count was adjusted to 0 for Cys, since they are all involved in disulfide bonds.

Experimentally, pi's were determined using Isogel agarose IEF plates, pH range
3-10 (FMC Bioproducts, Rockland, ME). A Biorad Bio-phoresis horizontal electrophoresis ceil

30 was used to run the IEF, following the directions of both manufacturers. The electrophoresis
conditions were: 500 volts (limiting), at 20 mA current and 1 0 W of constant power. Focusing
was complete in 90 min. IEF standards were purchased from Biorad; the kit included
phycocyanin, g-lactoglobulin B, bovine carbonic anhydrase, human carbonic anhydrase, equine
myoglobin, human hemoglobins A and C, 3 lentil lectins and cytochrome C, with pi values of

35 4.65, 5.10, 6.00, 6.50, 7.00, 7.10 and 7.50, 7.80, 8.00, and 8.20 and 9.60, respectively. Gels were
stained and destained according to the directions provided by FMC

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Quantitation of CC49 Antibody Species

All purified CC49 antibodies including the IgG, scFv2 species and the monomeric
scFv were quantitated by measuring the absorbence of protein dilutions at 280 mm using
matching 1.0 cm pathlength quartz cuvettes (Hellma) and a Perkin-Elmer UVA/IS
5 Spectrophotometer, Model 552A. Molar absorptivities (E m ) were determined for each
antibody by using the following formula:

E m = (number Trp)X 5,500 + (number Tyr)X 1,340 +
(number (Cys)2)X 150 + (number Phe) X 10
The values are based on information given by D. B. Wetlaufer, Advances in Protein Chemistry,

10 iL 375-378).

High Performance Liquid Chromatography

All high performance liquid chromatography (HPLC) was performed for CC49

scFv2 purification using an LKB HPLC system with titanium or teflon tubing throughout. The

system consists of the Model 2150 HPLC pump, model 2152 controller, UV CORD Sli model 2238
15 detection system set at an absorbence of 276 nm and the model 221 1 SuperRac fraction

collector.

PCR Generation of Subunits

All polymerase chain reactions (PCR) were performed with a reaction mixture
consisting of: 150 picograms (pg) plasmid target (pSCFVUHM); 100 pmoles primers; 1 pL

20 Perkin-Elmer-Cetus (PEC, Norwalk, CT) Ampli-Taq polymerase; 16pLof 10mMdNTPsand 10uL
of 10X buffer both supplied in the PEC kit; and sufficient water to bring the volume to total
volume to 1 00 ul. The PCR reactions were carried out essentially as described by the
manufacturer. Reactions were done in a PEC 9600 thermocycler with 30 cycles of : denaturation
of the DNA at 94°C for 20 to 45 sec, annealing from between 52 to 60°C for 0.5 to 1 .5 rnin., and

25 elongation at 72°C for 0.5 to 2.0 min. Oligonucleotide primers were synthesized on an Applied
Biosystems (Foster City, CA) 380A or 391 DNA synthesizer and purified as above.
Ligations

Ligation reactions using 1 00 ng of vector DNA and a corresponding 1 : 1
stoichiometric equivalent of insert DNA were performed using a Stratagene (La Jolla, CA) T4
30 DNA ligase kit following the manufacturer's directions. Ligation reactions (20 ul total volume)
were initially incubated at 18°Cand allowed to cool gradually overnight to 4°C.
Transformations

Transformations were performed utilizing 1 00 \xl of Stratagene E. coli AG 1
competent cells (Stratagene, La Jolla, CA) according to the directions provided by the
35 manufacturer. DNA from the ligation reactions (1-5 ul) were used. After the transformation
step, cells were allowed to recover for 1 hr in Luria broth (LB) at37°C with continuous mixing
and subsequently plated onto either 20 ug/mL chloramphenicol containing (CAM 20) Luria agar
for pSCFVUHM, p49LHLH or p49LHHLor 100 pg/mL ampicillin (AMP 100) Luria agar plates

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(LB-AMP 100) for clones containing the plasmid pSL301 or subsequent constructions derived
from pSL301.

Screening of E. coli Clones

Bacterial plasmids were isolated from LB broth culture containing the appropriate
5 drug to maintain selection pressure using Promega (Madison, Wl) Magic mini-prep plasmid

preparation kits. The kit was used per the manufacturer's specifications.

Plasmid Constructions

Two plasmids, designated p49LHLH and p49LHHL, were constructed to produce

multivalent single chain antibodies. The host cell containing p49LHLH produced a polypeptide
-j o which can be designated by V l -L-V h -L-V l -L-Vh where V L and V H are the light and heavy cahin

variable regions of CC49 antibody and linker (L) is a 25 amino acid linker having the sequence

(SEQIDNO: 5).

Leu-Ser-Ala-Asp-Asp-Ala-Lys-Lys-Asp-Ala-Ala-Lys-Lys-Asp-Asp-Ala-Lys-Lys-Asp-
-Asp-Ala-Lys-Lys-Asp-Leu.
1 5 The host cell containing p49LHHL produced a polypeptide which can be

designated by Vl-L-Vh-L-V h -L-Vl where V L and V H are the light and heavy chain variable
domains of the CC49 antibody and L is a peptide linker having the amino acid sequence
indicated above.

The nucleotide sequence (SEQ ID NO: 6) and amino acid sequence (5EQ ID NO: 7)

20 of the CC49 V L -L-V H -L-V L -L-V H (p49LHLH) are given in Figure 6. The nucleotide sequence (SEQ
ID NO: 8) and amino acid sequence (SEQ ID NO: 9) of the CC49 V L -L-V H -L-V H -L-V L (p49LHHL) are
given in Figure 7.
Construction of pSL301 HT

The construction of pSL301 HT is illustrated in Figure 8. The Bacillus lichiformis

25 penicillinase P (penP) terminator sequence was removed from the plasmid designated
pSCFV UHM by a 45 minute digest with Nhe I and BamH I, excised from a 4.5 percent
polyacrylamide gel after electrophoresis, electroeluted, ethanol precipitated and ligated into
the same sites in the similarly prepared vector: pSL301 (Invitrogen, San Diego, CA). A
procedure for preparing pSCFV UHM is given is U.S. patent application Ser. No. 07/935,695 filed

30 August 21, 1992, the disclosure of which is hereby incorporated by reference. In general,
pSCFV UHM contains a nucleotide sequence for a penP promoter; a unique Nco I restriction
site; CC49 V L region; Hind III restriction site; a 25 amino acid linker; a unique a Xho I restriction
site; CC49 Vh region; Nhe I restriction site; penP terminator; and BamH I restriction site (see.
Figure 8). The penP promoter and terminator are described in Mezes, etal. (1983),/ Biol.

35 Chem.,258, 11211-11218(1983).

An aliquot of the ligation reaction (3 ul) was used to transform competent E. coli
AG 1 cells which were plated on LB-AMP1 00 agar plates and grown overnight. Potential clones
containing the penP terminator insert were screened using a Pharmacia (Gaithersburg, MD) T7

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Quickprime 32 P DNA labeling kit in conjunction with the microwave colony lysis procedure
outlined in Buluwela et al., Nucleic Acid Research, 17, 452 (1989). The probe, which was the
penP-Nhe l-BamH I terminator fragment itself was prepared and used according to the
directions supplied with the Quickprime kit. A clone which was probe positive and which

5 contained the 207 base pair inserts from a BamH I and Nhe I digest (base pairs (bp) 1958 to
2165, Figure 6) was designated pSL301 Tand chosen to construct pSL301 HT which would
contain the nucleotide sequence for CC49 V H . The reason the Nhe l-BamH I penP terminator
was placed into pSL301 was to eliminate the Eco47 III restriction endonuclease site present in
the polylinker region between its Nhe i and BamH I sites. This was designed to accommodate

1 0 the subsequent build-up of the V L and V H domains where the Eco47 III site needed to be unique
for the placement of each successive V domain into the construction. As each V domain was
added at the Eco47 lll-Nhe I sites, the Eco47 111 was destroyed in each case to make the next
Eco47 III site coming in on the unique insert.

The V H sequence was made by PCR with oligos 5' SCP1 and 3'oligo SCP5 using

15 pSCFV UHM as the target for PCR amplification. The DNA sequence for 5CP1 (5EQ ID NO: 10)
and SCP5 (SEQ ID NO: 1 1) are as follows:

SCP 1 : S'-TAAA CTCGAG GTT CAG TTG CAG CAG -3 '

SCP5: S'-TAAA GCT AGC ACCA AGCGCT TAG TGA GGA GAC GGT GAC TGA GGT-3'
The underlined portion indicates the endonuclease restriction sites.
20 The amplified V H DNA was purified from a 4 percent PAG, electroeluted ethanol

precipitated and dissolved in 20 water. The Vh sequence was digested with Xho I and Nhe I
restriction enzymes and used as the insert with the p5L301 T vector which had been digested
with the same restriction enzymes and subsequently purified. A standard ligation reaction was
done and an aliquot (4 pL) used to transform competent E. coli AG1 cells. The transformed cells
25 were plated onto LB AMP100agar plates. Candidate clones were picked from a Nhe I and Xho I
digest screen that revealed that the CC49V H insert had been obtained.

DNA sequencing was performed to verify the sequence of the CC49Vh with
United States Biochemical (USB) (Cleveland, Ohio) Sequence kit and sequencing primers
p5L301SEQB (a 21 bp sequencing primer which annealed in the pSL301 vector 57 bp upstream
30 from the Xho I site) and CC49VHP, revealed clones with the correct CC49V H sequence in

pSL301 HT. This plasmid was used as the starting point in the construction of both pSL301 -HHLT
and pSL301-HLHT. The sequencing oligos used are shown here.

The nucleotide sequence of pSL301SEQ B (SEQ ID NO: 12) and CC49V H (SEQ ID
No: 13) are as follows:
35 pSL301SEQB: 5'-TCG TCC GAT TAG GCA AGCTTA-3"

CC49VHP: 5'-GAT GAT TTT AAA TAC AAT GAG-3'

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Example 1 p49LHHL Construction

Using pSL301 HT(5 jig) as the starting material, it was digested with Eco47 III and
Nhe I and the larger vector fragment was purified. A CC49V H insert fragment was generated
by PCR using SCP6C as the 5' oligo and SCP5 as the 3' oligo. The nucleotide sequence (SEQ ID
5 NO: 14) of SCP6B is as follows:

SCP6B : 5'- TAAA TGCGCA GAT GAC GCA AAG AAA G AC GCA GCT AAA AAA G AC GAT

GCC AAA AAG GAT GAC GCC AAG AAA GAT CTT GAG GTT CAG TTG CAG CAG

TCT-G'

The oligo SCP6B also contains part of the coding region for the linker (bp 8-76 of SEQ ID
10 NO: 14). The portion of the oligo designed to anneal with the CC49VH target in pSCFV UHM is

from bp77-90 in SEQ ID NO: 14.

The underlined sequence corresponds to the Fsp I site. The resulting PCR insert

was purified, digested with Fsp I and Nhe I and used in a ligation reaction with the pSL301 HT

Eco47 lll-Nhe I vector (Figure 7). Competent E. coli AG1 cells were used for the transformation
1 5 of this ligation reaction (3 pL) and were plated on LB-AMP1 00 agar plates. Two clones having

the correct size Xho l-Nhe I insert representative of the pSL301 HHT product were sequenced

with the oligo SQP1 and a single clone with the correct sequence (nucleotides 1 1 24-1 543 of

Figure 7) was chosen for further construction. The nucleotide sequence of SQP1 (SEQ ID

NO: 16) is as follows:
20 SQP1 : 5'-TG ACT TTA TGT AAG ATG ATG T-3'

The final linker-V L subunit(bp 1544-1963, Figure 7) was generated using the

5'oligo, SCP7b and the 3' oligo, SCP8a, using pSCFV UHM as the target for the PCR. The

nucleotide sequence of SCP7b (SEQ ID NO: 17 is as follows:

SCP7b: 5' -TAAA TGC GCA GAT GAC GCA AAG AAA GAC GCA GCT AAA AAA GAC GAT

25 GCC AAA AAG GAT GAC GCC AAG AAA GAT CTT GAC ATT GTG ATG TCA CAG TCT

CC

The underlined nucleotides correspond to an Fsp I site. The nucleotide sequence of SCP8a
(SEQ ID NO: 18) is as follows:

SCP8a : 5' -TAAA GCTAGC TTT TTA CTT AAG CAC CAG CTT GGT CCC-3'

30 The first set of underlined nucleotides correspond to an Nhe I site, while the other

corresponds to an Af I II site. Nucleotides 8-76 of SCP70 code for the linker (nucleotides
1544-1612 of Figure 7) while nucleotides 77-99 which anneal to the V L correspond to 1613-1635
of Figure 7. The primer SCP8a has a short tail at its 5' end, a Nhe I restriction site, a stop codon,
an Afl II restriction site and the last 21 bases of the V L . After Fsp 1 and Nhe I digestion, this

35 resulting 420 bp insert was purified and ligated into the Nhe 1 and Eco47 III sites of the purified
pSL301 HHT vector, candidate clones were screened with Nhe I and Xho I, the correct size insert
verified and sequenced with 49LFR2(-) and SQP1 to confirm the newly inserted sequence in
pSL301HHLT. The nucleotide sequence (SEQ ID NO: 19) is as follows:

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49LFR2(-): 5'-CTG CTG GTA CCA GGC CAA G-3'

The plasmid pSL301 HHLT was digested with Xho I and Nhe I, purified, and the
resulting 1179 bp V H -linker-V H -linker-V L segment ligated into pSCFV UHM, which had been cut
with the same restriction enzymes and the larger vector fragment purified, to form p49LHHL
5 The ligation reaction (4 aliquot) was used to transform competent E. col i AG 1 cells

(Stratagene) and plated onto LBCAM20 agar plates. A single clone which had a plasmid with
the correct restriction enzyme map was selected to contain p49LHHL The p49LHHL contains a
penP promoter and a nucleotide sequence forthe CC49 multivalent single chain antibody
scFv2:

! o V L -L-V H -L-V H -I-V L or CC49 scFv2 (LHHL).

Example 2 : p49LHLH Construction

The construction of p49LHLH is schematically represented in Figure 11. A linker-
V L subunit was generated with the 5' oligo SCP7b and the 3'oiigo SCP9.
SCP9: 5'-TAA A GC TAG CA C CA A GCG CTT AGT TTC AGC ACC AGCTTG GTCCCAG-3'

15 The SCP7b oligo (nucleotides 8-76) codes for the linker in Figure 6 (corresponding

to nucleotides 1 1 24-1 192) and annealed to the pSCFV UHM target for the PCR (nucleotides
77-99) corresponding to nucleotides 1 193-1 21 5 of the V in Figure 6.

SCP9 has a Nhe I site (first underlined nucleotides) and an Eco47 III site (second
underlined nucleotides) which are restriction sites needed for making the pSL301 HLT ready to

20 accept the next V domain. Nucleotides 18-23 of SCP9 correspond to nucleotides 1532-1537 of
Figure 6 (coding for the first 2 amino acids of the linker), while nucleotides 24-46 correspond to
nucleotides 1508-1531 of Figure 6 which was also the annealing region forSCP9 in the PCR. The
plasmid pSL301 HT was digested with Eco47 III and Nhe I and the larger vector fragment was
purified for ligation with the linker-CC49V L DNA insert fragment from the PCR which had been

25 treated with Fsp I and Nhe I and purified. The ligation mixture (3 pL) was used to transform
E. co//AG1 competent cells and one colony having the correct Xho l-Nhe I size fragment was
sequenced using the oligo PENPTSEQ2. The nucleotide sequence (5EQ. ID NO. 21) is as follows:

5'-TTG ATC ACC AAG TGA CTT TAT G-3'

The sequencing results indicated that there had been a PCR error and deletion in
30 the resulting pSL301 HT clone. A five base deletion, corresponding to nucleotides 1 533-1 537 as
seen in Figure 6 had been obtained and nucleotide 1531 which should have been a T was
actually a G, as determined from the DNA sequence data. The resulting sequence was

5'...G A AGCGCT T...etc.

where the underlined sequence fortuitously formed an Eco47 ill site. The
35 AGCGCT sequence in Figure 6, would correspond to nucleotides 1530, 1531, 1532, 1538, 1539
and 1540. This error was corrected in the next step, generating pSL301 HLHT, by incorporating
the 5 base deletion at the end of oligo SCP6C.

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SCP6C: 5'-TAAGCGCTGATGATGCTAAGAAGGACGCCGCAAAAAA

G GACGACG CAAAAAAAG ATG ATG CAAAAAAG G ATCTGG
AGGTTCAGTTGCAGCAGTCTGAC-3'
The underiined sequence in SCP6c corresponds to an Eco47 ill site. SCP6C was
5 used as the 5' oiigo, with SCP1 0 as the 3' oligo in a PCR to generate a linker CC49 V L segment.
The nucleotide sequence (SEQ ID NO: 23) is as follows:
5CP10: 5'TTG T GC TAG CT T TTT ATG AGG AGA CGG TGA CTG AGGTT-3'

The underlined sequence in SCP1 0 corresponds to the Nhe I site found at
nucleotides 1958-1963 in Figure 6. The PCR insert was digested this time only with Nhe land
10 purified. The vector (pSL301 HLT) wasdigested at the Eco47 III site (that had been formed) and
Nhe I and purified. The insert and vector were ligated and an aliquot (3 used to transform
competent E. coli AG 1 cells. This was plated on LB-AMP100 plates and candidate clones
screened with Xho I and Nhe I. Three clones having the correct size DNA were obtained. Two
of these clones were sequenced using the oligo 49VLCDR3( + ) and SQP1 . The nucleotide
1 5 sequence (DWQ ID NO: 24 of 49VLCDR3( + ) is as follows:

49VLCDR3( + ):

5'-CAG CAG TAT TAT AGC TAT-3'

One clone, with the correct sequence was obtai ned and the sequence from
nucleotides 1533 to 1963 in Figure 6 were verified, giving a correct pSL301 HLHL clone.

20 To generate the final plasmid, p49LHLH for expression inE. coli, pSL301 HLHT

(5 pg) was digested with Nhe I and Xho I, and the smaller insert fragment containing the
V H -L-V L -L-V H sequence purified. It was ligated with the larger purified vector fragment from a
digest of pSCFV UHM (5 pg) with Xho I and Nhe I. An aliquot of the ligation mix (4 yL) was used
to transform competent E. coli AG 1 cells. The transformation mix was plated on LB-CAM20

25 plates, and a representative clone for p49 LHLH was selected on the basis of a correct restriction
enzyme map (see Figure 10) and biological activity toward TAG-72.
Example 3 : Purification of CC49scFv2 LHLH and LHHLCovalently Linked Dimers

For the purification of the CC49 covalently linked single chain dimers, (scFv2) f
E. coli periplasmic fractions were prepared from 1 .0 L overnight cultures of both p49LHLH and

30 p49LHHL. Briefly, the culture was divided into 4 X 250 mL portions and centrifuged at
5,000 rpm for 10 minutes in a Sorvall GS-3 rotor. The pelleted cells were washed and
resuspended in 100 mL each of 10 mM Tris-HCI pH 7.3 containing 30 mM Nad. The cells were
again pelleted and washed with a total of 100 mL 30 mM Tris-HCI pH 7.3 and pooled into one
tube. To this, 100 mL of 30 mM Tris-HCI pH 7.3 c: raining 40 percent w/v sucrose and 2.0 mLof

IZ 1 0 mM EDTA dH 7.5 wes added. The mixture wa^ :ptat room temperature, with occasional
shaking, for 0 minxes. The hypertonic cells were then pelleted as before. In the next step, the
shock, the pellet was quickly suspended in 20 mL ice cold 0.5 mM MgCb and kept on ice for 10
minutes, with occasional shaking. The cells were pelleted as before and the supernatant

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containing the E. coli periplasmic fraction was clarified further by filtration through a 0.2 vim
Nalge (Rochester, NY) filter apparatus and concentrated in Amicon (Danvers, MA) Centriprep
30 and Centricon 30 devices to a vol ume of less than I.OmL

The concentrated periplasmic shockates from either the p49LHLH or p49LHHL

5 clones were injected onto a Pharmacia (Piscataway, NJ) Superdex75 HR 10/30 HPLC column that
had been equilibrated with PBS. At a flow rate of 0.5 mL/minute, the product of interest, as
determined by competition ELISA, had emerged between 21 through 24 minutes. The active
fractions were pooled, concentrated as before and dialyzed overnight using a system 500
Microdialyzer Unit (Pierce Chemical) against 20 mM Tris-HCI pH 7.6 with 3-4 changes of buffer

1 0 and using an 8,000 MW cut-off membrane. The sample was injected on a Pharmacia Mono Q
HR 5/5 anion exchange HPLC column. A gradient program using 20 mM Tris-HCI pH 7.6 as
buffer A and the same solution plus 0.5 M NaCI as buffer B was employed at a flow rate of
1 .5 mL/min. The products of interest in each case, as determined by competition ELISA,
emerged from the column between 3 and 4 minutes. Analysis of the fractions at this point on

T 5 duplicate SDS-PAGE gels, one stained with Coomassie Brilliant Blue R-250 and the other

transferred for Western analysis (using biotinylated FAID 14 as the probe antibody) revealed a
single band at the calculated molecular weight for the scFv2 (LHLH or LHHL) species at 58,239
daltons. The active fractions were in each case concentrated, dialysed against 50 mM MES pH
5.8 overnight and injected on a Pharmacia Mono S HR 5/5 cation exchange column. The two

20 fractions of interest from this purification step, as determined by SDS-PAGE and ELISA, fractions
5 and 6, eluted just before the start of the gradient, so they had not actually bound to the
column. Fractions 5 and 6 were consequently pooled for future purification.

A Mono Q column was again run on the active Mono S fractions but the buffer
used was 20 mM Tris-HCI, pH 8.0 and the flow rate was decreased to 0.8 mL/minute. The

25 products emerged without binding, but the impurity left over from the Mono S was slightly
more held up, so that separation did occur between 5 and 6 minutes. After this run, the
products were homogeneous and were saved for further characterization.
Isoelectric Focusing

The isoelectric points (pi) of the constructs was predicted using the DNASTAR
30 (Madison, WI) computer program Protein-titrate. Based on amino acid composition, a MW and
pi value was calculated.

Experimentally, pis were determined using FMC Bioproducts (Rockland, ME)
Isogel IEF plates, pH range 3-10. A Biorad (Richmond, CA) electrophoresis unit was used to run
the IEF, following the directions of both manufacturers. The electrophoresis conditions were as
35 follows: 500 V (limiting) at 20 mA and at 10 W of constant power. Focusing was complete in
90 minutes. Biorad IEF standards included phycocyanin, beta lactoglobulin B, bovine carbonic
anhydrase, human carbonic anhydrase, equine myoglobulin, human hemoglobins A and C, 3
lentil lectin, and cytochrome C with pi value of 4.65, 5. 1 0, 6.00, 6,50, 7.00, 7.50, 7.8, 8.00, 8.20

-20-

WO 94/13806

PCT/US93/12039

and 9.6, respectively. Gels were stained and destained according to directions provided by
FMC The DNASTAR program predicted values of 8.1 for the pi for both scFv2 species. A single,
homogeneous band for the pure products was observed on the gel at pi values for both at 6.9.

Purified CC49 antibodies such as the IgG, scFv2 (LHLH and LHHL) were quantitated

5 by measuring the absorbence spectrophotometrically at 280 nm. Molar absorbtivity values, cm*
were determined for each using the formula cited above by Wetlaufer.

Based on the amino acid composition, the E° - }% (280 nanometers) values for CC49
IgG, CC49 scFv2 LHLH, CC49scFv2 LHHL and CC49 scFvwere 1.49, 1.65, 1.65 and 1.71,
respectively.

10 Example 4

Relative activities of the CC49 scFv2 species LHLH and LHHL, were compared with
the IgG and a monomer scFvform with a FLAG peptide at the COOH terminus.

Percent competition was determined from the ELISA data by the following

equation:

Zero competition - sample reading (OD405-450 nm) „„
zero competition - 1 00 percent competition

The "zero competition" value was determined by mixing (1:1) one percent BSA
with the biotinylated CC49 (3 X 1 0-14 moles) while the 1 00 percent com petition value was
based on a 5 ng/mL sample of CC49 IgG mixed with the biotinylated CC49 IgG. The data are
presented in Figure 11. Absorbence values for the samples were measured at 405 nm - 450 nm.

20 The average of triplicate readings was used. Initially samples (25 pL) were applied to the
TAG-72 coated microliter plates at 1 .0 X 10-10 moles of binding sites/mL Biotinylated CC49
(4 pg/pL diluted 1 :20,000 - used 25 pL) diluted the samples by a factor of 2. Serial dilutions (1 :2)
were performed. Both forms of the scFv2 are approximately equivalent to the IgG (see
Figure 11). In a separate experiment, a CC49 scFv monomer was compared to a Fab fragment,

25 both of which are monovalent and these were also shown to be equivalent in their binding
affinity for TAG-72. These results indicate that both forms of the covalently linked dimers have
2 fully functional antigen binding sites. This is the same increase in avidity as observed with the
whole IgG, relative to a monomeric species.

These data also indicate that the scFv2 molecules, like their CC49 IgG parent are

30 candidates for immunotherapeutic applications, but with the benefit of increased capillary
permeability and more rapid biodistribution pharmacokinetics. The advantage should allow
multiple injections of compounds of the present invention and give higher tumor:tissue ratios
in immunotherapeutic treatment regimens for cancer treatment, relative to the existing IgG
molecules.

3 ^ Or K^r embodiments of the invention will be apparent to those skHied in the art

" s a considers -son of this specification or practice of the invention disclosed herein. It is

rrr>, ,«.y;

-21-

WO 94/13806

PCT/US93/12039

intended that the specification and examples be considered as exemplary only, with the true
scope and spirit of the invention being indicated by the following claims.

5

10

15

20

25

30

35

-22-

WO 94/13806

PCT/US93/12039

1 . A mutivalent single chain antibody which comprises two or more single
chain antibody fragments each fragment having affinity for an antigen wherein the fragments
are covalently linked by a first peptide linker and each fragment comprising:

(a) a first polypeptide comprising a light chain variable domain;
5 (b) a second polypeptide comprising a heavy chain variable domain; and

(c) a second peptide linker linking the first and second polypeptides into a
functional binding moiety.

2. The multivalent single chain antibody of Claim 1 wherein the first peptide
linker has the amino and sequence

1 o Leu Ser Ala Asp Asp Ala Lys Lys Asp Ala Ala Lys Lys Asp Asp Ala Lys Lys Asp Asp Ala Lys Lys

Asp Leu.

3. The multivalent single chain antibody of Claim 1 wherein the light chain
variable region has an amino acid sequence substantially the same as that of Figure 3 and the
heavy chain variable region has an amino acid sequence substantially the same as that of

15 Figures.

4. The multivalent single chain antibody of Claim 1 wherein the first and
second peptide linkers have an amino acid sequence which is substantially the same.

5. A DNA sequence which codes for a mutivalent single chain antibody, the
multivalent single antibody comprising two or more single chain antibody fragments, each

20 fragment having affinity for an antigen wherein the fragments are covalently linked by a first
peptide linker and each fragment comprising:

(a) a first polypeptide comprising a light chain variable domain;

(b) a second polypeptide comprising a heavy chain variable domain; and

(c) a second peptide linker linking the first and second polypeptides into a
25 functional binding moiety.

6. The DNA sequence of Claim 5 wherein the sequence coding for the first
polypeptide is substantially the same as that of Figure 2 and the sequence coding for the
second polypeptide is substantially the same as that of Figure 3.

30

35

-23-

WO 94/13806

PCT/US93/12039

FIGURE 1

! / 2 2

WO 94/13806

PCT/US93/12039

FIGURE 2

GAC

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2/22

WO 94/13806

PCT/US93/12039

FIGURE 3

Asp lie Val Met Ser Gin Ser Pro
Gly Glu Lys Val Thr Leu Ser Cys
Tyr Ser Gly Asn Gin Lys Asn Tyr
Pro Gly Gin Ser Pro Lys Leu Leu
Glu Ser Gly Val Pro Asp Arg Phe
Asp Phe Thr Leu Ser lie Ser Ser
Val Tyr Tyr Cys Gin Gin Tyr Tyr
Ala Gly Thr Lys Leu Val Leu Lys

Ser Ser Leu Pro Val Ser Val
Lys Ser Ser Gin Ser Leu Leu
Leu Ala Trp Tyr Gin Gin Lys
lie Tyr Trp Ala Ser Ala Arg
Thr Gly Ser Gly Ser Gly Thr
Val Lys Thr Glu Asp Leu Ala
Ser Tyr Pro Leu Thr Phe Gly

3/22

WO 94/13806

PCT/US93/12039

FIGURE 4

GAG GTT CAG TTG CAG CAG TCT GAC GCT GAG TTG GTG AAA CCT

GGG GCT TCA GTG AAG ATT TCC TGC AAG GCT TCT GGC TAC ACC

TTC ACT GAC CAT GCA ATT CAC TGG GTG AAA CAG AAC CCT GAA

CAG GGC CTG GAA TGG ATT GGA TAT TTT TCT CCC GGA AAT GAT

GAT TTT AAA TAC AAT GAG AGG TTC AAG GGC AAG GCC ACA CTG

ACT GCA GAC AAA TCC TCC AGC ACT GCC TAC GTG CAG CTC AAC

AGC CTG ACA TCT GAG GAT TCT GCA GTG TAT TTC TGT ACA AGA

TCC CTG AAT ATG GCC TAC TGG GGT CAA GGA ACC TCA GTC ACC

GTC TCC TCA

U / 2 2

WO 94/13806

PCT/US93/12039

Glu Val Gin Leu Gin
Ala Ser Val Lys lie
Asp His Ala lie His
Glu Trp lie Gly Tyr
Asn Glu Arg Phe Lys
Ser Ser Thr Ala Tyr
Ser Ala Val Tyr Phe
Gly Gin Gly Thr Ser

FIGURE 5

Gin Ser Asp Ala Glu
Ser Cys Lys Ala Ser
Trp Val Lys Gin Asn
Phe Ser Pro Gly Asn
Gly Lys Ala Thr Leu
Val Gin Leu Asn Ser
Cys Thr Arg Ser Leu
Val Thr Val Ser Ser

Leu Val Lys Pro Gly

Gly Tyr Thr Phe Thr

Pro Glu Gin Gly Leu

Asp Asp Phe Lys Tyr

Thr Ala Asp Lys Ser

Leu Thr Ser Glu Asp

Asn Met Ala Tyr Trp

5/22

WO 94/13806

PCT/US93/12039

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INTERNATIONAL SEARCH REPORT

Intern al Application No

PCT/US 93/12039

A. CLASSIFICATION OF SUBJECT MATTER

IPC 5 C12N15/13 C07K15/28 C12N15/62 A61K39/395

According to International Patent Classification (IPC) or to bote national classification and IPC

B. FIELDS SEARCHED

Minimum documentation searched (classification system followed by classification symbols)

IPC 5 C12N C07K

Documentation searched other than minimum documentation to the extent that such documents are included in the fields searched

Electronic data base consulted during the international search (name of data base and, where practical, search terms used)

C. DOCUMENTS CONSIDERED TO BE RELEVANT

Category *

Citation of document, with indication, where appropriate, of the relevant passages

Relevant to claim No.

x

Y
Y

WO, A, 91 19739 (CELLTECH LIMITED) 26
December 1991
see example 1

CANCER RESEARCH

vol. 52, no. 12 , 15 June 1992 ,
PHILADELPHIA, PA, USA
pages 3402 - 3408

T.YOKATA ET AL. 'Rapid tumour penetration
of a single-chain Fv and comparison with
other immunoglobulin forms'
see page 3403, column 1, paragraph 4

-/—

1,5

2-4,6

3,6

LI

Further documents are listed in the continuation of box C.

HI

Patent family members are listed in annex.

* Special categories of cited documents :

"A" document defining the general state of the art which is not
considered to be of particular relevance

*E* earlier document but published on or after the international
filing date

"L* document which may throw doubts on priority claim(s) or
which is cited to establish the publication date of another
citation or other special reason (as specified)

"O" document referring to an oral disclosure, use, exhibition or
other means

"P* document published prior to the international filing date but
later than the priority date claimed

T" later document published after the international filing date
or priority date and not in conflict with the application but
cited to understand the principle or theory underlying the
invention

'X" document of particular relevance; the claimed invention
cannot be considered novel or cannot be considered to
involve an inventive step when the document is taken alone

'Y* document of particular relevance; the claimed invention
cannot be considered to involve an inventive step when the
document is combined with one or more other such docu-
ments, such combination being obvious to a person skilled
in the art.

"&* document member of the same patent family

Date of the actual completion of the international search

25 March 1994

Date of mailing of the international search report

27 -0V 1L

Name and mailing address of the ISA

European Patent Office, P.B. 5818 Patentlaan 2
NL - 2280 HV Rijswijk
Tel. ( + 31-70) 340-2040, Tx. 31 651 eo*i al,
Fax: (+31-70) 340-3016

Authorized officer

Cupido, M

Form PCT/1S A/210 (second iheet) (July 19Si)

page 1 of 2

INTERNATIONAL SEARCH REPORT

Intem/ U Application No

PCT/US 93/12039

C(Continuauon) DOCUMENTS CONSIDERED TO BE RELEVANT

Category

Citation of document, with indication, where appropriate, of the relevant passages

Relevant to claim No.

P,X

BIOCHEMISTRY

vol. 30, no. 42 , 22 October 1991 ,

EASTON , PA US

pages 10117 - 10125

M.W.PANTOLIANO ET AL. 'Conformational

stability, folding and 1 igand-binding

affinity of single-chain Fv immunoglobulin

fragments expressed in Escherichia coli 1

cited in the application

see page 10120, column 1, paragraph 2

EP,A,0 506 124 (TANOX BIOSYSTEMS, INC.) 30
September 1992
see example 4

W0, A, 93 11161 (ENZ0N, INC.) 10 June 1993
see figure 19A

2,4

1.5

1,3-6

Form PCT/ISA/210 (continuation of second iheet) (July 1993)

page 2 of 2

INTERNATIONAL SEARCH REPORT

imormation on patent family members

Intern U Application No

PCT/US 93/12039

Patent document

Publication

Patent family

Publication

cited in search report

date

member(s)

date

WO-A-9 119739

26-12-91

AU-A-

7983191

07-01-92

EP-A-

0486652

27-05-92

GB-A-

2250995

24-06-92

JP-T-

5502039

15-04-93

EP-A-0506124

30-09-92

AU-B-

640863

02-09-93

AU-A-

1299292

15-10-92

JP-A-

5117164

14-05-93

WO-A-9311161

10-06-93

AU-A-

3178993

28-06-93

Form PCT/1S A/210 (patent family annex} (July 1992)

CORRECTED
VERSION*

WORLD INTELLECTUAL PROPERTY ORGANIZATION

International Bureau

PCT

INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT)

(51) International Patent Classification 5 :

C12N 15/13, C07K 15/28, C12N 15/62,
A61K 39/395

Al

(11) International Publication Number:
(43) International Publication Date:

WO 94/13806

23 June 1994 (23.06.94)

(21) International Application Number:

FCT/US93/12039

(22) International Filing Date:

10 December 1993 (10.12.93)

(30) Priority Data:

07/990,263

11 December 1992 (11.12.92) US

(71) Applicant: THE DOW CHEMICAL COMPANY [US/US];

2030 Dow Center, Abbott Road, Midland, MI 48640 (US).

(72) Inventors: MEZE S, Peter, S.; 25 Sill Lane, Oldlyme, CT 06371

(US). GOURLIE, Brian, B.; 3713 Orchard Drive, Midland,
Mi 48640 (US).

(74) Agent: ULMER, Duane, C; The Dow Chemical Company,
Patent Department, P.O. Box 1967, Midland, MI 48641-
1967 (US).

(81) Designated States: AU, CA, JP, European patent (AT, BE,
CH, DE, DK, ES, FR, GB, GR, IE, IT, LU, MC, NL, PT,
SE).

Published

With international search report.

Before the expiration of the time limit for amending the
claims and to be republished in the event of the receipt of
amendments.

(54) Title: MULTIVALENT SINGLE CHAIN ANTIBODIES

(57) Abstract

The present invention discloses
multivalent single chain antibodies
which have two or more biologically
active antigen binding sites. The
multivalent single chain antibodies
are formed by using a peptide linker
to covalently link two or more single
chain antibodies, each single chain
antibody having a variable light domain
linked to a variable heavy chain domain
by a peptide linker.

Schematic Representation Of Covalently &
Non-Covalently Linked Single Chain Fv Multimers

L L L COOH

SCFv2 (LHLH)

HOOC

L L~~ L
scFv2 (LHHL)

-COOH

NH 2

COOH

Fv2

* (Referred to in PCT Gazette No. 19/1994, Section 11)

FOR THE PURPOSES OF INFORMATION ONLY

Codes used to identify States party to the PCT on the front pages of pamphlets publishing international
applications under the PCT.

AT

Austria

GB

United Kingdom

MR

Mauritania

AU

Australia

GE

Georgia

MW

Malawi

BB

Barbados

GN

Guinea

NE

Niger

BE

Belgium

GR

Greece

NL

Netherlands

BF

Burkina Faso

HU

Hungary

NO

Norway

BG

Bulgaria

IE

Ireland

NZ

New Zealand

BJ

Benin

IT

Italy

PL

Poland

BR

Brazil

JP

Japan

PT

Portugal

BY

Belarus

KE

Kenya

RO

Romania

CA

Canada

KG

Kyrgystan

RU

Russian Federation

CF

Central African Republic

KP

Democratic People's Republic

SD

Sudan

CG

Congo

of Korea

SE

Sweden

CH

Switzerland

KR

Republic of Korea

SI

Slovenia

CI

Cote d*l voire

KZ

Kazakhstan

SK

Slovakia

CM

Cameroon

LI

Liechtenstein

SN

Senegal

CN

China

LK

Sri Lanka

TD

Chad

cs

Czechoslovakia

LU

Luxembourg

TG

Togo

cz

Czech Republic

LV

Latvia

TJ

Tajikistan

DE

Germany

MC

Monaco

TT
UA

Trinidad and Tobago

DK

Denmark

MD

Republic of Moldova

Ukraine

ES

Spain

MG

Madagascar

US

United States of America

Fl

Finland

ML

Mali

uz

Uzbekistan

FR

France

MN

Mongolia

VN

Viet Nam

GA

Gabon

WO 94/13806 PCT/US93/12039

MULTIVALENT SINGLE CHAIN ANTIBODIES

The present invention relates to single chain multivalent antibodies.
Antibodies are proteins belonging to a group of immunoglobulins elicited by the
5 immune system in response to a specific antigen or substance which the body deems foreign.
There are five classes of human antibodies, each class having the same basic structure. The
basic structure of an antibody is a tetramer, or a multiple thereof, composed of two identical
% heterodimers each consisting of a light and a heavy chain. The light chain is composed of one
variable (V) and one constant (Q domain, while a heavy chain is composed of one variable and
10 three or more constant domains. The variable domains from both the light and heavy chain,
designated V L and V H respectively, determine the specificity of an immunoglobulin, while the
constant (C) domains carry out various effector functions.

Amino acid sequence data indicate that each variable domain comprises three
complementarity determining regions (CDR) flanked by four relatively conserved framework
15 regions (FR). The FR are thought to maintain the structural integrity of the variable region
domain. The CDR have been assumed to be responsible for the binding specificity of individual
antibodies and to account for the diversity of binding of antibodies.

As the basic structure of an antibody contains two heterodimers, antibodies are
multivalent molecules. For example, the IgG classes have two identical antigen binding sites,
20 while the pentameric igM class has 10 identical binding sites.

Monoclonal antibodies having identical genetic parentage and binding specificity
have been useful both as diagnostic and therapeutic agents. Monoclonal antibodies are
routinely produced by hybridomas generated by fusion of mouse lymphoid cells with an
appropriate mouse myeloma cell line according to established procedures. The administration
25 of murine antibodies for in vivo therapy and diagnostics in humans is limited however, due to
the human anti-mouse antibody response illicited by the human immune system.

■

Chimeric antibodies, in which the binding or variable regions of antibodies
derived from one species are combined with the constant regions of antibodies derived from a
different species, have been produced by recombinant DNA methodology. See, for example,

30 Sahagen et al., J. Immunol., 137 : 1 066-1 074 (1 986); Sun et aL, Proc. Natl. Acad. Sci. USA,

82:214-218(1987); Nishimura etal.. Cancer Res., 47:999-1005(1987); and Lieet al. Proc Natl.
Acad. Sci. USA, 84:3439-3443 (1987) which disclose chimeric antibodies to tumor-associated
antigens. Typically, the variable region of a murine antibody is joined with the constant region
of a human antibody. It is expected that as such chimeric antibodies are largely human in

35 composition, they will be substantially less immunogenic than murine antibodies.

Chimeric antibodies still carry the Fc regions which are not necessary for antigen
binding, but constitute a major portion of the overall antibody structure which affects its
pharmacokinetics. For the use of antibodies in immunotherapy or immunodiagnostics, is it

-1-

WO 94/13806

PCT/US93/12039

desirable to have antibody-like molecules which localize and bind to the target tissue rapidly
and for the unbound material to quickly clear from the body. Generally, smaller antibody
fragments have greater capillary permeability and are more rapidly cleared from the body
than whole antibodies.

5 Since it is the variable regions of light and heavy chains that interact with an

antigen, single chain antibody fragments (scFvs) have been created with one V L and one V H ,
containing all six CDR's, joined by a peptide linker (U.S. Patent 4,946,778) to create a V L -l-V H
polypeptide, wherein the L stands for the peptide linker. A scFv wherein the V L and V H
domains are orientated V H -L-V L is disclosed in U.S. Patent 5,132,405.

10 As the scFvs have one binding site as compared to the minimum of two for

complete antibodies, the scFvs have reduced avidity as compared to the antibody containing
two or more binding sites.

It would therefore be advantageous to obtain constructions of scFvs having more
than one binding site to enhance the avidity of the polypeptide, and retain or increase their

j 5 antigen recognition properties. In addition, it would be beneficial to obtain multivalent scFvs
which are bispecific to allow for recognition of different epitopes on the target tissue, to allow
for antibody-based recruitment of other immune effector functions, or allow antibody capture
of a therapeutic or diagnostic moiety.

It has been found that single chain antibody fragments, each having one V H and

20 one V L domain covalently linked by a first peptide linker, can be covalently linked by a second
peptide linker to form a multivalent single chain antibody which maintains the binding affinity
of a whole antibody. In one embodiment, the present invention is a multivalent single chain
antibody having affinity for an antigen wherein the multivalent single chain antibody
comprises two or more light chain variable domains and two or more heavy chain variable

25 domains; wherein, each variable domain is linked to at least one other variable domain.

In another embodiment, the present invention is a multivalent single chain antibody
which comprises two or more single chain antibody fragments, each fragment having affinity
for an antigen wherein the fragments are covalently linked by a first peptide linker and each
frag m ent com pri si ng :

30 (a) a first polypeptide comprising a light chain variable domain;

(b) a second polypeptide comprising a heavy chain variable domain; and

(c) a second peptide linker linking the first and second polypeptides into a functional
binding moiety.

In another embodiment, the invention provides a DNA sequence which codes for
35 a multivalent single chain antibody, the multivalent single chain antibody comprising two or
more single chain antibody fragments, each fragment having affinity for an antigen wherein
the fragments are covalently linked by a first peptide linker and each fragment comprising:
(a) a first polypeptide comprising a light chain variable domain;

WO 94/13806

PCT/US93/12039

(b) a second polypeptide comprising a heavy chain variable domain; and

(c) a second peptide linker linking the first and second polypeptides into a functional
binding moiety.

The multivalent single chain antibodies allow for the construction of an antibody
5 fragment which has the specificity and avidity of a whole antibody but are smaller in size

allowing for more rapid capillary permeability. Multivalent single chain antibodies also allow
for the construction of a multivalent single chain antibody wherein the binding sites can be
two different antigenic determinants.
BRIEF DESCRIPTION OF THE DRAWINGS
-jq Figure 1 illustrates covalently linked single chain antibodies having the

configuration V L -L-V H -L-V L -L-V H (LHLH) and V L -L-V H -L-V H -L-V L (LHHL) and a noncovalently
linked Fv single chain antibody (Fv2).

Figure 2 illustrates the nucleotide sequence of CC49 V L .
Figure 3 illustrates the amino acid sequence of CC49 V L .
^ 5 Figure 4 illustrates the nucleotide sequence of CC49 Vh-

Figure 5 illustrates the amino acid sequence of CC49 V H .

Figure 6 illustrates the nucleotide sequence and amino acid sequence of the CC49
single chain antibody LHLH in p49LHLH.

Figure 7 illustrates the nucleotide sequence and amino acid sequence of the CC49
20 single antibody LHHL in p49LHHL

Figure 8 illustrates construction of plasmids pSL301 T and pSL301 HT.
Figure 9 illustrates construction of plasmid p49LHHL.
Figure 10 illustrates construction of plasmid p49LHLH.

Figure 11 illustrates the resuitsof a competition assay using CC^9 IgG, CC49 scFv2,
25 and CC49 scFv using biotinylated CC49 IgG as competitor.

The entire teaching of all references cited herein are hereby incorporated by

reference.

Nucleic acids, amino acids, peptides, protective groups, active groups and such,
when abbreviated, are abbreviated according to the IUPAC IUB (Commission on Biological
30 Nomenclature) or the practice in the fields concerned.

The term "single chain antibody fragment" (scFv) or "antibody fragment" as used
herein means a polypeptide containing a V L domain linked to a V H domain by a peptide linker
(L), represented by V L -L-V H . The order of the V L and V H domains can be reversed to obtain
polypeptides represented as Vh-L-V l . "Domain" is a segment of protein that assumes a discrete
35 function, such as antigen binding or antigen recognition.

A "multivalent single chain antibody" means two or more single chain antibody
fragments covalently linked by a peptide linker. The antibody fragments can be joined to form
bivalent single chain antibodies having the order of the V L and V H domains as follows:

-3-

r

WO 94/13806

PCT/US93/12039

V l -L-Vh-L-V l -L-V H ; V l -L-V h -L-V h -L-V l ; V h -L-V l -L-V h -L-V l ; or V H -L-V L -L-V L -L-V H .
Single chain multivalent antibodies which are trivalent and greater have one or more antibody
fragments joined to a bivalent single chain antibody by an additional interpeptide linker. In a
preferred embodiment, the number of Vj_ and Vh domains is equivalent.

5 The present invention also provides for multivalent single chain antibodies which

can be designated V H -L-V H -L-V L -L-V L or V l -L-V l -L-V h -L-\/h.

Covalently linked single chain antibodies having the configuration V L -L-V H -L-V L -L-
-V H (LHLH) and V L -L-V H -L-V H -L-V L (LHHL) are illustrated in Figure 1 . A noncovalentiy linked Fv
single chain antibody (Fv2) is also illustrated in Figure 1.

1 o The single chain antibody fragments for use in the present invention can be

derived from the light and/or heavy chain variable domains of any antibody. Preferably, the
light and heavy chain variable domains are specific for the same antigen. The individual
antibody fragments which are joined to form a multivalent single chain antibody may be
directed against the same antigen or can be directed against different antigens.

1 5 To prepare a vector containing the DNA sequence for a single chain multivalent

antibody, a source of the genes encoding for these regions is required. The appropriate DNA
sequence can be obtained from published sources or can be obtained by standard procedures
known in the art. For example, Kabat et aL, Sequences of Proteins of Immunological Interest
4thed. L (\99}), published by The U.S. Department of Health and Human Services, discloses

20 sequences of most of the antibody variable regions which have been described to date.

When the genetic sequence is unknown, it is generally possible to utilize cDNA
sequences obtained from mRNA by reverse transcriptase mediated synthesis as a source of DNA
to clone into a vector. For antibodies, the source of mRNA can be obtained from a wide range
of hybridomas. See, for example, the catalogue ATCC Cell Lines and Hybridomas, American

25 Type Culture Collection, 20309 Parklawn Drive, Rockville Md., USA (1990). Hybridomas

secreting monoclonal antibodies reactive with a wide variety of antigens are listed therein, are
available from the collection, and usable in the present invention. These cell lines and others of
similar nature can be utilized as a source of mRNA coding for the variable domains or to obtain
antibody protein to determine amino acid sequence of the monoclonal antibody itself.

i

30 Variable regions of antibodies can also be derived by immunizing an appropriate

vertebrate, normally a domestic animal, and most conveniently a mouse. The immunogen will
be the antigen of interest, or where a hapten, an antigenic conjugate of the hapten to an
antigen such as keyhole limpet hemocyanin (KLH). The immunization may be carried out
conventionally with one or more repeated i njections of the immunogen into the host mammal,

35 normally at two to three week intervals. Usually, three days after the last challenge, the spleen
is removed and dissociated into single ceils to be used for cell fusion to provide hybridomas
from which mRNA can readily be obtained by standard procedures known in the art.

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When an antibody of interest is obtained, and only its amino acid sequence is
known, it is possible to reverse translate the sequence.

The V L and Vh domains for use in the present invention are preferably obtained
from one of a series of CC antibodies against tumor-associated glycoprotein 72 antigen

5 (TAG-72) disclosed in published PCT Application WO 90/04410 on May 3, 1990, and published
PCT Application WO 89/00692 on January 26, 1989. More preferred are the V L and V H domains
from the monoclonal antibody designated CC49 in PCT Publications WO 90/0441 0 and
WO 89/00692. The nucleotide sequence (SEQ ID NO: 1) which codes for the V L of CC49 is
substantially the same as that given in Figure 1. The amino acid sequence (SEQ ID NO: 2) of the

1 0 V L of CC49 is substantially the same as that given in Figu re 2. The nucleotide sequence (SEQ ID
WO: 3) which codes for the V H of CC49 is substantially the same as that given in Figure 3. The
amino acid sequence (SEQ ID NO: 4) for the V H of CC49 is substantially the same as that given in
Figure 4.

To form the antibody fragments and multivalent single chain antibodies of the

1 5 present invention, it is necessary to have a suitable peptide linker. Suitable linkers for joining
the Vh and V L domains are those which allow the Vh and V L domains to fold into a single
polypeptide chain which will have a three dimensional structure very similar to the original
structure of a whole antibody and thus maintain the binding specificity of the whole antibody
from which antibody fragment is derived. Suitable linkers for linking the scFvs are those which

20 allow the linking of two or more scFvs such that the V H and V L domains of each

immunoglobulin fragment have a three dimensional structure such that each fragment
maintains the binding specificity of the whole antibody from which the immunoglobulin
fragment is derived. Linkers having the desired properties can be obtained by the method
disclosed in U.S. Patent 4,946,778, the disclosure of which is hereby incorporated by reference.

25 From the polypeptide sequences generated by the methods described in the 4,946,778, genetic
sequences coding for the polypeptide can be obtained.

Preferably, the peptide linker joining the Vh and V L domains to form a scFv and
the peptide linker joining two or more scFvs to form a multivalent single chain antibody have
substantially the same amino acid sequence.

30 It is also necessary that the linker peptides be attached to the antibody fragments

such that the binding of the linker to the individual antibody fragments does not interfere with
the binding capacity of the antigen recognition site.

A preferred linker is based on the helical linker designated 205C as disclosed in
Pantoliano etal. Biochem., 30, 101 17-10125 (1991) but with the first and last amino acids

35 changed because of the codon dictated by the Xho I site at one end and the Hind III site at the
other. The amino acid sequence (SEQ ID NO: 5) of the preferred linker is as follows:

Leu-Ser-Ala-Asp-Asp-Ala-Lys-Lys-Asp-Ala-Ala-Lys-Lys-Asp-Asp-Ala-Lys-Lys-Asp-Asp-Ala-

-Lys-Lys-Asp-Leu.

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The linker is generally 10 to 50 amino acid residues. Preferably, the linker is 10 to
30 amino acid residues. More preferably the linker is 12 to 30 amino acid residues. Most
preferred is a linker of 1 5 to 25 amino acid residues.

Expression vehicles for production of the molecules of the invention include

5 plasmids or other vectors. In general, such vectors contain replicon and control sequences
which are derived from species compatible with a host cell. The vector ordinarily carries a
replicon site, as well as specific genes which are capable of providing phenotypic selection in
transformed cells. For example, £. coli is readily transformed using pBR322 [Bolivar etaL, Gene,
2,95- (1977), orSambrook etaL, Molecular Cloning, Cold Spring Harbor Press, New York, 2nd

10 Ed. (1989)].

Plasmids suitable for eukaryotic cells may also be used. S. cerevisiae, or common
baker's yeast, is the most commonly used among eukaryotic microorganisms, although a
number of other strains, such as Pichia pastoris, are available. Cultures of cells derived from
multicellular organisms such as SP2/0 or Chinese Hamster Ovary (CHO), which are available from

1 5 the ATCC, may also be used as hosts. Typical of vector plasmids suitable for mammalian cells
are pSV2neo and pSV2gpt (ATCC); pSVL and pKSV-1 0 (Pharmacia), pBPV-1/pML2d
(International Biotechnology, Inc.).

The use of prokaryotic and eukaryotic viral expression vectors to express the
genes for polypeptides of the present invention is also contemplated.

20 It is preferred that the expression vectors and the inserts which code for the single

chain multivalent antibodies have compatible restriction sites at the insertion junctions and
that those restriction sites are unique to the areas of insertion. Both vector and insert are
treated with restriction endonucleases and then ligated by any of a variety of methods such as
those described in Sambrook et aL, supra.

25 Preferred genetic constructions of vectors for production of single chain

multivalent antibodies of the present invention are those which contain a constitutively active
transcriptional promoter, a region encoding signal peptide which will direct synthesis/secretion
of the nascent single chain polypeptide out of the cell. Preferably, the expression rate is
commensurate with the transport, folding and assembly steps to avoid accumulation of the

30 polypeptide as insoluble material. In addition to the replicon and control sequences,

additional elements may also be needed for optimal synthesis of single chain polypeptide.
These elements may include splice signals, as well as transcription promoter, enhancers, and
termination signals. Furthermore, additional genes and their products may be required to
facilitate assembly and folding (chaperones).

35 Vectors which are commercially available can easily be altered to meet the above

criteria for a vector. Such alterations are easily performed by those of ordinary skill in the art in
light of the available literature and the teachings herein.

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Additionally, it is preferred that the cloning vector contain a selectable marker,
such as a drug resistance marker or other marker which causes expression of a selectable trait
by the host cell. "Host cell" refers to cells which can be recombinantly transformed with vectors
constructed using recombinant DNA techniques. A drug resistance or other selectable marker

5 is intended in part to facilitate in the selection of transformants. Additionally, the presence of
a selectable marker, such as a drug resistance marker, may be of use in keeping contaminating
microorganisms from multiplying in the culture medium. In this embodiment, such a pure
culture of the transformed host cell would be obtained by culturing the cells under conditions
which require the induced phenotype for survival.

-jq Recovery and purification of the present invention can be accomplished using

standard techniques known in the art. For example, if they are secreted into the culture
medium, the single chain multivalent antibodies can be concentrated by ultrafiltration. When
the polypeptides are transported to the periplasmic space of a host cell, purification can be
accomplished by osmotically shocking the cells, and proceeding with ultrafiltration, antigen

T 5 affinity column chromatography or column chromatography using ion exchange

chromatography and gel filtration. Polypeptides which are insoluble and present as refractile
bodies, also called inclusion bodies, can be purified by lysis of the cells, repeated centrifugation
and washing to isolate the inclusion bodies, solubilization, such as with guanidine-HCI, and
refolding followed by purification of the biologically active molecules.

20 The activity of single chain multivalent antibodies can be measured by standard

assays known in the art, for example competition assays, enzyme-linked immunosorbant assay
(ELISA), and radioimmunoassay (RIA).

The multivalent single chain antibodies of the present invention provide unique
benefits for use in diagnostics and therapeutics. The use of multivalent single chain antibodies

25 afford a number of advantages over the use of larger fragments or entire antibody molecules.
They reach their target tissue more rapidly, and are cleared more quickly from the body.

For diagnostic and/or therapeutic uses, the multivalent single chain antibodies
can be constructed such that one or more antibody fragments are directed against a target
tissue and one or more antibody fragments are directed against a diagnostic or therapeutic

30 a 9 ent -

The invention also concerns pharmaceutical compositions which are particularly
advantageous for use in the diagnosis and/or therapy of diseases, such as cancer, where target
antigens are often expressed on the surface of cells. For diagnostic and/or therapeutic uses, the
multivalent single chain antibodies can be conjugated with an appropriate imaging or
35 therapeutic agent by methods known in the art. The pharmaceutical compositions of the
invention are prepared by methods known in the art, e.g., by conventional mixing, dissolving
or lyophilizing processes.

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The invention will be further clarified by a consideration of the following
examples, which are intended to be purely exemplary of the present invention.

5

10

15

20

25

30

35

-8-

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ABBREVIATIONS

10

15

20

25

30

BCIP
bp

Bis-Tris
propane

BSA

CDR

ELISA

Fv2

IEF

Kbp

LB

Mab

MES

NBT

Oligo

PAG

PAGE

PBS

PCR

pSCFV

RIGS

RIT

SCFv

SCFv2

SDS
TBS
Tris
TTBS

V H
Vl

5-bromo-4-chloro-3-indoyl phosphate
base pair

( 1 , 3-bis [ tr is (hydroxymethyl ) -methyl ami no] -
propane)

bovine serum albumin
Complementarity determining region
enzyme linked immunosorbent assay
non-covalent single chain Fv dimer
isoelectric focusing
kilo base pair
Luria-Bertani medium
monoclonal antibody

2-(N-Morpholino)ethane sulfonic acid

molecular weight

nitro blue tetrazolium chloride

Oligonucleotides

polyacrylamide gel

polyacrylamide gel electrophoresis

phosphate buffered saline

polymerase chain reaction

plasmid containing DNA sequence coding for SCFV
radio immunoguided surgery
r ad i o i nununo t he r apy

single chain Fv immunoglobulin fragment monomer

single chain Fv immunoglobulin fragment dimer
covalently linked

sodium dodecyl sulfate

Tr is-buf fered saline

(Tristhydrox y me t hy 1 ] am i no me t hane )

Tween-20 wash solution

immunoglobulin heavy chain variable domain
immunoglobulin light chain variable domain

35

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Antibodies

CC49: A murine monoclonal antibody specific to the human tumor-associated
glycoprotein 72 (TAG-72) deposited as ATCC No. HB9459.

CC49 FAB : An antigen binding portion of CC49 consisting of an intact light chain

5 linked to the N-terminal portion of the heavy chain.

CC49 scFv : Single chain antibody fragment consisting of two variable domains of
CC49 antibody joined by a peptide linker.

CC49 Fv2 : Two CC49 scFv non-covalently linked to form a dimer. The number
after Fv refers to the number of monomer subunits of a given molecule, e.g., CC49 Fv6 refers to
10 thehexamermultimers.

CC49 scFv2 : Covalently-linked single chain antibody fragment consisting of two
CC49 V L domains and two V H domains joined by three linkers. Six possible combinations for the
order of linking the V L (L) and the V H (H) domains together are: LHLH, LHHL, LLHH, HLLH, HLHL,
and HHLL
15 Piasmids

dSCFV UHM : Plasmid containing coding sequence for scFv consisting of a CC49
variable light chain and a CC49 variable heavy chain joined by a 25 amino acid linker.

P49LHLH or P49LHHL : Piasmids containing the coding sequence for producing
CC49 scFv2 LHLH or LHHL products, respectively.
20 EXAMPLES

General Experimental

Procedures for molecular cloning are as those described in Sambrook et al. v
Molecular Cloning, Cold Spring Harbor Press, New York, 2nd Ed. (1989) and Ausubel et al.,
Current Protocols in Molecular Biology, John Wiley and Sons, New York (1 992), the disclosures
25 of which are hereby incorporated by reference.

All water used throughout was deionized distilled water.
Oligonucleotide Synthesis and Purification

All oiigonuclotides (oligos) were synthesized on either a Model 380A or a
Model 391 DNA Synthesizer from Applied Biosystems (Foster City,CA) using standard
30 P-cyanoethyl phosphoramidites and synthesis columns. Protecting groups on the product were
removed by heating in concentrated ammonium hydroxide at 55°Cfor 6 to 15 hours. The
ammonium hydroxide was removed through evaporation and the crude mixtures were
resuspended in 30 to 40 ul of sterile water. After electrophoresis on polyacrylamide-urea gels,
the oligos were visualized using short wavelength ultraviolet (UV) light. DNA bands were
35 excised from the gel and eluted into 1 mL of 100 mM Tris-HCI, pH 7.4, 500 mM NaCI, 5 mM EDTA
over 2 hours at 65°C. Final purification was achieved by applying the DNA to Sep-Pac™ C-18
columns (Millipore, Bedford, MA) and eluting the bound oligos with 60 percent methanol. The

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solution volume was reduced to approximately 50 pL and the DNA concentration was
determined by measuring the optical density at 260 nm (OD 26Q ).
Restriction Enzyme Digests

All restriction enzyme digests were performed using Bethesda Research

5 Laboratories (Gaithersburg, MD) # New England Biolabs, Inc. (Beverly, MA) or Boehringer
Mannheim (BM, Indianapolis, IN) enzymes and buffers following the manufacturer's
recommended procedures. Digested products were separated by polyacrylamide gel
electrophoresis (PAGE). The gels were stained with ethidium bromide, the DNA bands were
visualized using long wavelength U V light and the DNA bands were then excised. The gel slices

10 were placed In dialysis tubing (Union Carbide Corp., Chicago) containing 5 mM Tris, 2.5 mM
acetic acid, 1 mM EDTA, pH 8.0 and eluted using a Max Submarine electrophoresis apparatus
(Hoefer Scientific Instruments, CA). Sample volumes were reduced on a Speed Vac
Concentrator (Savant Instruments, Inc., NY). The DNA was ethanol precipitated and redissolved
in sterile water.

15 Enzyme Linked Immunosorbent Assay (ELISA)

TAG-72 antigen, prepared substantially as described by Johnson et al, Can. Res.,
46. 850-857 (1986), was adsorbed onto the wells of a polyvinyl chloride 96 well microtiter plate
(Dynatech Laboratories, Inc., Chantilly, VA) by drying overnight. The plate was blocked with
1 percent BSA in PBS for 1 hour at 31°C and then washed 3 times with 200 pL of PBS,

20 0.05 percent Tween-20. 25 pL of test antibodies and 25 piL of biotinylated CC49 (1/20,000

dilution of a 1 mg/mL solution) were added to the wells and the plate incubated for 30 minutes
at 31°C. The relative amounts of TAG-72 bound to the plate, biotinylated CC49, streptavidin-
alkaiine phosphatase, and color development times were determined empirically in order not
to have excess of either antigen or biotinylated CC49, yet have enough signal to detect

25 competition by scFv. Positive controls were CC49 at 5 pg/mL and CC49 Fab at 1 0 pg/m L.

Negative controls were 1 percent BSA in PBS and/or concentrated LB. Unbound proteins were
washed away. 50 pL of a 1 : 1000 dilution of streptavidin conjugated with alkaline phosphatase
(Southern Biotechnology Associates, Inc., Birmingham, AL) were added and the plate was
i ncu bated for 30 minutes at 3 1°C. The plate was washed 3 more times. 50pLof a

30 para-nitrophenyl-phosphate solution (Kirkegaard & Perry Laboratories, Inc., Gaithersburg, MD)
were added and the color reaction was allowed to develop for a minimum of 20 minutes. The
relative amount of scFv2 binding was measured by optical density scanning at 404-450 nm
using a microplate reader (Molecular Devices Corporation, Manlo Park, CA). Binding of the
scFv2 species resulted in decreased binding of the biotinylated CC49 with a concomitant

35 decrease in color development.
SDS-PAGE and Western Blotting

Samples for SDS-PAGE analysis (20 pL) were prepared by boiling in a non-reducing
sample preparation buffer-Seprasol I (Integrated Separation Systems (ISS), Natick, MA) for

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5 minutes and loaded on 10-20 percent gradient poiyacrylamide Daiichi Minigelsas per the
manufacturer's directions (ISS).

Electrophoresis was conducted using a Mini 2-gel apparatus (ISS) at 55 mA per gel
at constant current for approximately 75 minutes. Gels were stained in Coomassie Brilliant Blue

5 R-250 (Bio-Rad, Richmond, CA) for at least 1 hour and destained. Molecular weight standards
were prestained (Mid Range Kit, Diversified Biotech, Newton Center, MA) and included the
following proteins: Phosphorylase b, glutamate dehydrogenase, ovalbumin, lactate
dehydrogenase, carbonic amhydrase, B-lactoglobulin and cytochrome C The corresponding
MWsare: 95,500, 55,000, 43,000, 36,000, 29,000, 18,400, and 12,400, respectively.

1 0 When Western analyses were conducted, a duplicate gel was also run. After

electrophoresis, one of the gels was equilibrated for 1 5-20 minutes in anode buffer #1 (0.3 M
Tris-HCI pH 10.4). An tmmobilon-P PVDF (polyvinylidenedichlorine) membrane (Millipore,
Bedford, MA) was treated with methanol for 2 seconds, and immersed in water for 2 minutes.
The membrane was then equilibrated in anode buffer #1 for 3 minutes. A Milliblot-SDE

1 5 apparatus (Millipore) was utilized to transfer proteins in the gel to the membrane. A drop of
anode buffer #1 was placed in the middle of the anode electrode surface. A sheet of Whatman
3MM filter paper was soaked in anode buffer #1 and smoothly placed on the electrode surface.
Another filter paper soaked in anode buffer #2 (25 mM tris pH 10.4) was placed on top of the
first one. A sandwich was made by next adding the wetted PVDF membrane, placing the

20 equilibrated gel on top of this and finally adding a sheet of filter paper soaked in cathode
buffer (25mM Tris-HCI, pH 9.4 in 40 mM glycine). Transfer was accomplished in 30 minutes
using 250 mA constant current (initial voltage ranged from 8-20 volts).

After blotting, the membrane was rinsed briefly in water and placed in a dish
with 20 mL blocking solution (1 percent bovine serum albumin (BSA) (Sigma, St. Louis, MO) in

25 Tris-buffered saline (TBS)). TBS was purchased from Pierce Chemical (Rockford, IL) as a

preweighed powder such that when 500 mL water is added, the mixture gives a 25 mM Tris,
0.15 M sodium chloride solution at pH 7.6. The membranes were blocked for a minimum of

1 hour at ambient temperature and then washed 3 times for 5 minutes each using 20 mL

0.5 percent Tween-20 wash solution (TTBS). To prepare the TTBS, 0.5mL of Tween 20 (Sigma)
30 wasmixed per liter of TBS. The probe antibody used was 20 mL biotinylated FAID 14 solution
(1 0 pg per 20 mL antibody buffer). Antibody buffer was made by adding 1 g BSA per 1 00 mL of
TTBS. After probing for 30-60 minutes at ambient temperature, the membrane was washed
3 times with TTBS, as above.

Next, the membrane was incubated for 30-60 minutes at ambient temperature
35 with 20 mL of a 1 :500 dilution in antibody buffer of streptavidin conjugated with alkaline
phosphatase (Southern Biotechnology Associates, Birmingham, AL). The wash step was again
repeated after this, as above. Prior to the color reaction, membranes were washed for

2 minutes in an alkaline carbonate buffer (20 mL). This buffer is 0. 1 M sodium bicarbonate,

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1 mM MgCi 2 -H 2 0, pH 9.8. To make up the substrate for alkaline phosphatase, nitroblue
tetrazoiium (NBT) chloride (50 mg, Sigma) was dissolved in 70 percent dimethylformamide.
5-Bromo-4-chioro-3-indoyl phosphate (BCIP) (25 mg, Sigma) was separately dissolved in
100 percent dimethylformamide. 5-Bromo-4-chloro-3-indoyl phosphate (BCIP) 25 mg, Sigma)
5 was separately dissolved in 100 percent dimethylformamide. These solutions are also
commercially available as a Western developing agent sold by Promega. For color
development, 120 piL of each were added to the alkaline solution above and allowed to react
for 1 5 minutes before they were washed from the developed membranes with water.
Biotinvlated FA1D14

10 FA1D14 is a murine anti-idiotypic antibody (lgG2a, Kisotype) deposited asATCC

No. CRL 10256 directed against CC49. FAID14 was purified using a Nygene Protein A affinity
column (Yonkers, NY). The manufacturer's protocol was followed, except that 0.1 M sodium
citrate, pH 3.0 was used as the eiution buffer. Fractions were neutralized to pH ~7 using 1.0 M
Tris-HCI pH 9.0. The biotinylation reaction was set up as follows. FAID14(1 mg, 100pLin

! 5 water) was mixed with 100 jiL of 0.1 M Na 2 C0 3 pH 9.6. Biotinyl-e-amino-caproic acid N-hydroxy
succinimide ester (Biotin-X-NHS) (Calbiochem, LaJolla, CA) (2.5 mg) was dissolved in 0.5 mL
dimethyisulfoxide. Biotin-X-NHS solution (20 pL) was added to the FAID1 4 solution and
allowed to react at 22°C for 4 hours. Excess biotin and impurities were removed by gel
filtration, using a Pharmacia Superose 12 HR10/30 column (Piscataway, NJ). At a flow rate of

20 0.8 mL/min, the biotinylated FAID14 emerged with a peak at 16.8min. The fractions making up
this peak were pooled and stored at 4°C and used to detect the CC49 idiotype as determined by
the CC49 V, and V u CDRs.
Isoelectric Focusing (IEF)

Isoelectric points (pi's) were predicted using a computer program called PROTEIN-

25 -TITRATE, available through DNASTAR (Madison, Wl). Based on amino acid composition with
an input sequence, a MW value is given, in addition to the pi. Since Cys residues contribute to
the charge, the count was adjusted to 0 for Cys, since they are all involved in disulfide bonds.

Experimentally, pi's were determined using Isogei agarose IEF plates, pH range
3-10 (FMC Byproducts, Rockland, ME). A Biorad Bio-phoresis horizontal electrophoresis cell

30 was used to run the IEF, following the directions of both manufacturers. The electrophoresis
conditions were: 500 volts (limiting), at 20 mA current and 10Wof constant power. Focusing
was complete in 90 min. IEF standards were purchased from Biorad; the kit included
phycocyanin, 0-lactoglobulin B, bovine carbonic anhydrase, human carbonic anhydrase, equine
myoglobin, human hemoglobins A and C, 3 lentil lectins and cytochrome C, with pi values of

35 4.65, 5.10, 6.00, 6.50, 7.00, 7.10 and 7.50, 7.80, 8.00, and 8.20 and 9.60, respectively. Gels were
stained and destained according to the directions provided by FMC.

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Quantitation of CC49 Antibody Species

All purified CC49 antibodies including the IgG, scFv2 species and the monomeric
scFvwere quantitated by measuring the absorbence of protein dilutions at 280 mm using
matching 1.0 cm pathlength quartz cuvettes (Hellma) and a Perkin-Elmer UV/VIS
5 Spectrophotometer, Model 552A. Molar absorptivities (E m ) were determined for each
antibody by using the following formula:

E m = (number Trp)X 5,500 + (number Tyr)X 1,340 +
(number (Cys)2) X 150 + (number Phe) X 10
The values are based on information given by D. B. Wetlaufer, Advances in Protein Chemistry,

10 1L 375-378).

High Performance Liquid Chromatography

All high performance liquid chromatography (HPLC) was performed for CC49

scFv2 purification using an LKB HPLC system with titanium or teflon tubing throughout. The

system consists of the Model 21 50 HPLC pump, model 21 52 controller, UV CORD Sll model 2238
1 5 detection system set at an absorbence of 276 nm and the model 221 1 SuperRac fraction

collector.

PCR Generation of Subunits

All polymerase chain reactions (PCR) were performed with a reaction mixture
consisting of: 1 50 picograms (pg) plasmid target (pSCFVUHM); 1 00 pmoles primers; 1 pL

20 Perkin-Eimer-Cetus (PEC, Norwalk, CT) Ampli-Taq polymerase; 16jiLof lOmMdIMTPsand 10 u.L
of 10X buffer both supplied in the PEC kit; and sufficient water to bring the volume to total
volume to 100ul. The PCR reactions were carried out essentially as described by the
manufacturer. Reactions were done in a PEC 9600 thermocycler with 30 cycles of: denaturation
of the DNA at 94°C for 20 to 45 sec, annealing from between 52 to 60°C for 0.5 to 1 .5 min., and

25 elongation at 72°C for 0.5 to 2.0 min. Oligonucleotide primers were synthesized on an Applied
Biosystems (Foster City, CA) 380A or 391 DNA synthesizer and purified as above.
Ligations

Ligation reactions using 1 00 ng of vector DNA and a corresponding 1 : 1
stoichiometric equivalent of insert DNA were performed using a Stratagene (La Jolla, CA) T4
30 DNA ligase kit following the manufacturer's directions. Ligation reactions (20 uL total volume)
were initially incubated at 18°C and allowed to cool gradually overnight to 4°C
Transformations

Transformations were performed utilizing 1 00 pL of Stratagene E. coli AG 1
competent cells (Stratagene, La Jolla, CA) according to the directions provided by the
35 manufacturer. DNA from the ligation reactions (1-5 uL) were used. After the transformation
step, cells were allowed to recover for 1 hr in Luria broth (LB) at 37°C with continuous mixing
and subsequently plated onto either 20 pg/mL chloramphenicol containing (CAM 20) Luria agar
for pSCFVUHM, p49LHLH or p49LHHL or 1 00 u.g/mL ampicillin (AMP 1 00) Luria agar plates

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■

(LB-AMP 100) for clones containing the plasmid pSL301 or subsequent constructions derived
from pSL301.

Screening of E. coli Clones

Bacterial plasmids were isolated from LB broth culture containing the appropriate
5 drug to maintain selection pressure using Promega (Madison, Wl) Magic mini-prep plasmid

preparation kits. The kit was used per the manufacturer's specifications.

Plasmid Constructions

Two plasmids, designated p49LHLH and p49LHHL f were constructed to produce

multivalent single chain antibodies. The host cell containing p49LHLH produced a polypeptide
10 which can be designated by V L -L-V H -L-V L -L-V H where V L and V H are the light and heavy cahin

variable regions of CC49 antibody and linker (L) is a 25 amino acid linker having the sequence

(SEQ!DNO:5).

Leu-Se r- Al a- Asp- Asp-AI a- Lys- Ly s- Asp-Al a- Al a- Lys- Lys- Asp- Asp- Al a- Ly s- Ly s- Asp-

-Asp- Al a- Lys-Lys- Asp- Leu .
1 5 The host cell containing p49LHHL produced a polypeptide which can be

designated by V L -L-V H -L-V H -L-V L where V u and V H are the light and heavy chain variable
domains of the CC49 antibody and L is a peptide linker having the amino acid sequence
indicated above.

The nucleotide sequence (SEQ ID NO: 6) and amino acid sequence (SEQ ID NO: 7)
20 of the CC49 V l -L-Vh-L-V l -L-V h (p49LHLH) are given in Figure 6. The nucleotide sequence (SEQ
ID NO: 8) and amino acid sequence (SEQ ID NO: 9) of the CC49 V L -L-V H -L-V H -L-V L (p49LHHL) are
given in Figure 7.
Construction of PSL301 HT

The construction of pSL301 HT is illustrated in Figure 8. The Bacillus Hchiformis
25 penicillinase P (penP) terminator sequence was removed from the plasmid designated
pSCFV UHM by a 45 minute digest with Nhe I and BamH I, excised from a 4.5 percent
polyacryiamide gel after electrophoresis, electroeluted, ethanol precipitated and ligated into

L

the same sites in the similarly prepared vector: pSL301 (Invitrogen, San Diego, CA). A
procedure for preparing pSCFV UHM is given is U.S. patent application Ser. No. 07/935,695 filed

30 August21, 1992, the disclosure of which is hereby incorporated by reference. Ingenerai,
pSCFV UHM contains a nucleotide sequence for a penP promoter; a unique Nco I restriction
site; CC49 V L region; Hind Hi restriction site; a 25 amino acid linker; a unique a Xho I restriction
site; CC49 V H region; Nhe I restriction site; penP terminator; and BamH I restriction site (see,
Figure 8). The penP promoter and terminator are described in Mezes, et al. (1983), J. Biol.

35 Chem., 258, 11211-11218(1983).

An aliquot of the ligation reaction (3 \xl) was used to transform competent E. coli
AG 1 cells which were plated on LB-AM P1 00 agar plates and grown overnight. Potential clones
containing the penP terminator insert were screened using a Pharmacia (Gaithersburg, MD) T7

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Quickprime 32 P DNA labeling kit in conjunction with the microwave colony lysis procedure
outlined in Buluwela et al., Nucleic Acid Research, 17, 452 (1989). The probe, which was the
penP-Nhe l-BamH I terminator fragment itself was prepared and used according to the
directions supplied with the Quickprime kit. A clone which was probe positive and which

5 contained the 207 base pair inserts from a BamH I and Nhe I digest (base pairs (bp) 1 958 to
2165, Figure 6) was designated pSL301 Tand chosen to construct pSL301 HT which would
contain the nucleotide sequence for CC49 V H . The reason the Nhe 1-BamH I penP terminator
was placed into pSL301 was to eliminate the Eco47 Ml restriction endonuclease site present in
the polylinker region between its Nhe I and BamH I sites. This was designed to accommodate

!0 the subsequent build-up of the V L and V H domains where the Eco47 111 site needed to be unique
for the placement of each successive V domain into the construction. As each V domain was
added at the Eco47 lll-Nhe I sites, the Eco47 III was destroyed in each case to make the next
Eco47 III site coming in on the unique insert.

The V H sequence was made by PCR with oligos 5' SCP1 and 3'oligo SCP5 using

15 pSCFVUHM as the target for PCR amplification. The DNA sequence for SCP1 (5EQID NO: 10)
and SCP5 (SEQ ID NO: 1 1) are as follows:

SCP1: 5'-TAAA CTCGAG GTT CAG TTG CAG CAG -3'

SCP5: y-TAAA GCTAGC ACCA AGCGCT TAG TGA GGA GAC GGT GAC TGA GGT-3'
The underlined portion indicates the endonuclease restriction sites.
20 The amplified Vh DNA was purified from a 4 percent PAG, electroeluted ethanol

precipitated and dissolved in 20 water. The Vh sequence was digested with Xho I and Nhe I
restriction enzymes and used as the insert with the pSL301 T vector which had been digested
with the same restriction enzymes and subsequently purified. A standard ligation reaction was
done and an aliquot (4 pL) used to transform competent E. coli AG1 cells. The transformed cells
25 were plated onto LB AMP1 00 agar plates. Candidate clones were picked from a Nhe I and Xho I
digest screen that revealed that the CC49Vh insert had been obtained.

DNA sequencing was performed to verify the sequence of the CC49Vh with
United States Biochemical (USB) (Cleveland, Ohio) Sequence kit and sequencing primers
pSL301SEQB (a21 bp sequencing primer which annealed in the pSL301 vector 57 bp upstream
30 from the Xho I site) and CC49VHP, revealed clones with the correct CC49V H sequence in

pSL301 HT. This plasmid was used as the starting point in the construction of both pSL301-HHLT
and pSL301-HLHT. The sequencing oligos used are shown here.

The nucleotide sequence of pSL301SEQ B (SEQ ID NO: 12) and CC49V H (SEQ ID
No: 13) are as follows:
35 pSL301SEQB: 5'-TCG TCC GAT TAG GCA AGCTTA-3"

CC49VHP: 5'-GAT GAT TTT AAA TAC AAT GAG-3'

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Example 1 p49LHHL Construction

Using pSL301 HT (5 pig) as the starting material, it was digested with Eco47 III and
Nhe I and the larger vector fragment was purified. A CC49V H insert fragment was generated
by PCR using SCP6C as the 5' oligo and SCP5 as the 3' oligo. The nucleotide sequence (SEQ ID
5 NO: 14) of SCP6B is as follows:

SCP6B : 5'- TAAA TGCGCA GAT GAC GCA AAG AAA G AC GCA GCT AAA AAA G AC GAT

GCC AAA AAG GAT GAC GCC AAG AAA GAT CTT GAG GTT CAG TTG CAG CAG

TCT-G'

The oligo SCP6B also contains part of the coding region for the linker (bp 8-76 of SEQ ID
10 NO: 14). The portion of the oligo designed to anneal with the CC49VH target in pSCFV UHM is

from bp77-90 in SEQ ID NO: 14.

The underlined sequence corresponds to the Fsp I site. The resulting PCR insert

was purified, digested with Fsp I and Nhe I and used in a ligation reaction with the pSL301 HT

Eco47 lll-Nhe I vector (Figure 7). Competent E. coli AG 1 cells were used for the transformation
! 5 of this ligation reaction (3 jiL) and were plated on LB-AM P1 00 agar plates. Two clones having

the correct size Xho l-Nhe I insert representative of the pSL301 HHT product were sequenced

with the oligo SQP1 and a single clone with the correct sequence (nucleotides 1124-1543 of

Figure 7) was chosen for further construction. The nucleotide sequence of SQP1 (SEQ ID

NO: 16) is as follows:
20 SQP1 : 5'-TG ACT TTA TGT AAG ATG ATG T-3'

The final linker-V L subunit(bp 1544-1963, Figure 7) was generated using the

5 # oligo, SCP7b and the 3' oligo, SCP8a, using pSCFV UHM as the target for the PCR. The

nucleotide sequence of SCP7b (SEQ ID NO: 17 is as follows:

SCP7b: S'-TAAA TGCGCA GAT GAC GCA AAG AAA GAC GCA GCT AAA AAA GAC GAT

25 GCC AAA AAG GAT GAC GCC AAG AAA GAT CTT GAC ATT GTG ATG TCA CAG TCT

CC

The underlined nucleotides correspond to an Fsp I site. The nucleotide sequence of SCP8a
(SEQ ID NO: 18) is as follows:

SCP8a : S'-TAAA GCTAGC TTT TTA CTT AAG CAC CAG CTT G GT CCC-3'

30 The first set of underlined nucleotides correspond to an Nhe I site, while the other

corresponds to an Af I II site. Nucleotides 8-76 of SCP70 code for the linker (nucleotides
1544-1612 of Figure 7) while nucleotides 77-99 which anneal to the V L correspond to 1613-1635
of Figure 7. The primer SCP8a has a short tail at its 5' end, a Nhe I restriction site, a stop codon,
an Afl II restriction site and the last 21 bases of the V L . After Fsp I and Nhe I digestion, this

35 resulting 420 bpinsertwas purified and ligated into the Nhe I and Eco47 III sites of the purified
pSL301 HHT vector, candidate clones were screened with Nhe I and Xho I, the correct size insert
verified and sequenced with 49LFR2(-) and SQP1 to confirm the newly inserted sequence in
pSL301HHLT. The nucleotide sequence (SEQ ID NO: 19) is as follows:

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49LFR2(~): 5'-CTG CTG GTA CCA GGC CAA G-3'

The plasmid pSL301 HHLT was digested with Xho I and Nhe I, purified, and the
resulting 1 179 bp V H -linker-V H -linker-V L segment ligated into pSCFV UHM, which had been cut
with the same restriction enzymes and the larger vector fragment purified, to form p49LHHL.
5 The ligation reaction (4 piL aliquot) was used to transform competent E. coli AG1 cells

(Stratagene) and plated onto LBCAM20 agar plates. A single clone which had a plasmid with
the correct restriction enzyme map was selected to contain p49LHHL The p49LHHL contains a
penP promoter and a nucleotide sequence for the CC49 multivalent single chain antibody
scFv2:

10 v L -L-V H -L-V H -L-V L orCC49scFv2(LHHL).

Example 2 : p49LHLH Construction

The construction of p49LHLH is schematically represented in Figure 1 1 . A linker-
Vl subunit was generated with the 5' oligo SCP7b and the 3'oligo SCP9.
SCP9: S'-TAA A G C TAG CA C CA A GCG CTT AGT TTC AGC ACC AGC TTG GTCCCAG-3'

1 5 The SCP7b oligo (nucleotides 8-76) codes for the linker in Figure 6 (corresponding

to nucleotides 1 1 24-1 1 92) and annealed to the pSCFV UHM target for the PCR (nucleotides
77-99) corresponding to nucleotides 1 193-1215of the VJn Figure 6.

SCP9 has a Nhe I site (first underlined nucleotides) and an Eco47 111 site (second
underlined nucleotides) which are restriction sites needed for making the pSL301 HLT ready to

20 accept the next V domain. Nucleotides 18-23 of SCP9 correspond to nucleotides 1532-1537 of
Figure 6 (coding for the first 2 amino acids of the linker), while nucleotides 24-46 correspond to
nucleotides 1 508-1 531 of Figure 6 which was also the annealing region for SCP9 in the PCR. The
plasmid pSL301 HT was digested with Eco47 III and Nhe I and the larger vector fragment was
purified for ligation with the linker-CC49V L DNA insert fragment from the PCR which had been

25 treated with Fsp I and Nhe I and purified. The ligation mixture (3 pL) was used to transform
E. coli AG1 competent cells and one colony having the correct Xho l-Nhe I size fragment was
sequenced using the oligo PENPTSEQ2. The nucleotide sequence (SEQ. ID NO. 21) is as follows:

5'-TTG ATC ACC AAG TGA CTT TAT G-3'

The sequencing results indicated that there had been a PCR error and deletion in
30 the resulting pSL301 HT clone. A five base deletion, corresponding to nucleotides 1 533-1 537 as
seen in Figure 6 had been obtained and nucleotide 1 531 which should have been a T was
actually a G, as determined from the DNA sequence data. The resulting sequence was

5'...G A AGC GCT T...etc.

where the underlined sequence fortuitously formed an Eco47 III site. The
35 AGCGCT sequence in Figure 6, would correspond to nucleotides 1530, 1531, 1532, 1538, 1539
and 1 540. This error was corrected in the next step, generating pSL301 HLHT, by incorporating
the 5 base deletion at the end of oligo SCP6C.

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SCP6C: 5'-TAAGCGCTGATGATGCTAAGAAGGACGCCGCAAAAAA

GGACGACGCAAAAAAAGATGATGCAAAAAAGGATCTGG
AGGTTCAGTTGCAGCAGTCTGAC-3'
The underlined sequence in SCP6c corresponds to an Eco47 III site. SCP6C was
5 used as the 5' oligo, with SCP10 as the 3' oligo in a PCRto generate a linker CC49 V L segment.
The nucleotide sequence (SEQ ID NO: 23) is as follows:
SCP1 0: 5'TTG T GCTAGCT T TTT ATG AGG AGA CGG TGA CTG AGG TT-3'

The underlined sequence in SCP 10 corresponds to the Nhe I site found at
nucleotides 1958-1963 in Figure 6. The PCR insert was digested this time only with Nhe I and
1 0 purified. The vector (pSL301 HLT) was digested at the Eco47 III site (that had been formed) and
Nhe I and purified. The insert and vector were ligated and an aliquot (3 pL) used to transform
competent E. coli AG 1 cells. This was plated on LB-AMP100 plates and candidate clones
screened with Xho I and Nhe I. Three clones having the correct size DNA were obtained. Two
of these clones were sequenced using the oligo 49VLCDR3( + ) and SQP1 . The nucleotide
1 5 sequence (DWQ ID NO: 24 of 49VLCDR3( + ) is as follows:

49VLCDR3( + ):

5'-CAG CAG TAT TAT AGC TAT-3'

One clone, with the correct sequence was obtained and the sequence from
nucleotides 1533 to 1963 in Figure 6 were verified, giving a correct pSL301 HLHL clone.

20 Togenerate the final plasmid, p49LHLH for expression in E. coli, pSL301 HLHT

(5 jig) was digested with Nhe I and Xho I, and the smaller insert fragment containing the
V h -L-V l -L-Vh sequence purified. It was ligated with the larger purified vector fragment from a
digest of pSCFV UHM (5 pig) with Xho I and Nhe I. An aliquot of the ligation mix (4 pL) was used
to transform competent E. coli AG1 cells. The transformation mix was plated on LB-CAM20

25 plates, and a representative clone for p49 LHLH was selected on the basis of a correct restriction
enzyme map (see Figure 10) and biological activity toward TAG-72.
Example 3 : Purification of CC49 scFv2 LHLH and LHHL Covalently Linked Dimers

For the purification of the CC49 covalently linked single chain dimers, (scFv2),
£. coli periplasmic fractions were prepared from 1 .0 L overnight cultures of both p49LHLH and

30 p49LHHL. Briefly, the culture was divided into 4 X 250 mL portions and centrifuged at
5,000 rpm for 10 minutes in a Sorvall GS-3 rotor. The pelleted cells were washed and
resuspended in 100 mL each of 10mMTris-HCI pH 7.3 containing 30 mM NaCI. The ceils were
again pelleted and washed with a total of 100 mL 30 mM Tris-HCI pH 7.3 and pooled into one
tube. To this, 100 mL of 30 mM Tris-HCI pH 7.3 containing 40 percent w/v sucrose and 2.0mLof

35 1 0 mM EDTA pH 7.5 was added. The mixture was kept at room temperature, with occasional
shaking, for 10 minutes. The hypertonic cells were then pelleted as before. In the next step, the
shock, the pellet was quickly suspended in 20 mL ice cold 0.5 mM MgCIa and kept on ice for 10
minutes, with occasional shaking. The cells were pelleted as before and the supernatant

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containing the £ coli periplasmic fraction was clarified further by filtration through a 0.2 um
Nalge (Rochester, NY) filter apparatus and concentrated in Amicon (Danvers, MA) Centriprep
30 and Centricon 30 devices to a volume of less than 1 .0 mL

The concentrated periplasmic shockates f rom either the p49LHLH or p49LHHL

5 clones were injected onto a Pharmacia (Piscataway, NJ) Superdex75 HR 10/30 HPLC column that
had been equilibrated with PBS. At a flow rate of 0.5 mL/minute, the product of interest, as
determined by competition ELISA, had emerged between 21 through 24 minutes. The active
'fractions were pooled, concentrated as before and diaiyzed overnight using a system 500
Microdialyzer Unit (Pierce Chemical) against 20 mM Tris-HCI pH 7.6 with 3-4 changes of buffer

1 o and using an 8,000 MW cut-off membrane. The sample was injected on a Pharmacia Mono Q
HR 5/5 anion exchange HPLC column. A gradient program using 20 mM Tris-HCI pH 7.6 as
buffer A and the same solution plus 0.5 M NaCI as buffer B was employed at a flow rate of
1.5 mL/min. The products of interest in each case, as determined by competition ELISA,
emerged from the column between 3 and 4 minutes. Analysis of the fractions at this point on

! 5 duplicate SDS-PAGE gels, one stained with Coomassie Brilliant Blue R-250 and the other

transferred for Western analysis (using biotinylated FAID 14 as the probe antibody) revealed a
single band at the calculated molecular weight for the scFv2 (LHLHor LHHL) species at 58,239
daltons. The active fractions were in each case concentrated, dialysed against 50 mM MES pH
5.8 overnight and injected on a Pharmacia Mono S HR 5/5 cation exchange column. The two

20 fractions of interest from this purification step, as determined by SDS-PAGE and ELISA, fractions
5 and 6, eluted just before the start of the gradient, so they had not actually bound to the
column. Fractions 5 and 6 were consequently pooled for future purification.

A Mono Q column was again run on the active Mono S fractions but the buffer
used was 20 mM Tris-HCI, pH 8.0 and the flow rate was decreased to 0.8 mL/minute. The

25 products emerged without binding, but the impurity left over from the Mono S was slightly
more held up, so that separation did occur between 5 and 6 minutes. After this run, the
products were homogeneous and were saved for further characterization.
Isoelectric Focusing

The isoelectric points (pi) of the constructs was predicted using the DNASTAR
30 (Madison, Wl) computer program Protein-titrate. Based on amino acid composition, a MW and
pi value was calculated.

Experimentally, pis were determined using FMC Bioproducts (Rockland, ME)
Isogel IEF plates, pH range 3-10. A Biorad (Richmond, CA) electrophoresis unit was used to run
the IEF, following the directions of both manufacturers. The electrophoresis conditions were as
35 follows: 500 V (limiting) at20mA and at 10 W of constant power. Focusing was complete in
90 minutes. Biorad IEF standards included phycocyanin, beta lactogiobulin B, bovine carbonic
anhydrase, human carbonic anhydrase, equine myoglobulin, human hemoglobins A and C, 3
lentil lectin, and cytochrome C with pi value of 4.65, 5.10, 6.00, 6,50, 7.00, 7.50, 7.8, 8.00, 8.20

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and 9.6, respectively. Gels were stained and destained according to directions provided by
FMC The DNASTAR program predicted values of 8.1 for the pi for both scFv2 species. A single,
homogeneous band for the pure products was observed on the gel at pi values for both at 6.9.

Purified CC49 antibodies such as the lgG r scFv2 (LHLH and LHHL) were quantitated

5 by measuring the absorbence spectrophotometrically at 280 nm. Molar absorbtivity values, em,
were determined for each using the formula cited above by Wetlaufer.

Based on the amino acid composition, the E° 1% (280 nanometers) values for CC49
lgG,CC49scFv2 LHLH, CC49scFv2 LHHL and CC49scFvwere 1.49, 1.65, 1.65 and 1.71,
respectively.

10 Example 4

Relative activities of the CC49 scFv2 species LHLH and LHHL, were compared with
the IgG and a monomer scFv form with a FLAG peptide at the COOH terminus.

Percent competition was determined from the ELISAdata by the following

equation:

Zero competition - sample reading (OD405-450 nm) xl0Q
1 5 zero competition - 1 00 percent competition

The "zero competition" value was determined by mixing (1 : 1) one percent BSA
with the biotinylated CC49(3 X 10-14 moles) while the 100 percent competition value was
based on a 5 pg/mL sample of CC49 IgG mixed with the biotinylated CC49 IgG. The data are
presented in Figure 1 1 . Absorbence values for the samples were measured at 405 nm - 450 nm.

20 The average of triplicate readings was used. Initially samples (25 pL) were applied to the
TAG-72 coated microliter plates at 1.0 X 10-10 moles of binding sites/mL. Biotinylated CC49
(4 ixg/pL diluted 1 :20,000 - used 25 jiL) diluted the samples by a factor of 2. Serial dilutions (1:2)
were performed. Both forms of the scFv2 are approximately equivalent to the IgG (see
Figure 11). In a separate experiment, a CC49 scFv monomer was compared to a Fab fragment,

25 both of which are monovalent and these were also shown to be equivalent in their binding
affinity for TAG-72. These results indicate that both forms of the covalently linked dimers have
2 fully functional antigen binding sites. This is the same increase in avidity as observed with the
whole IgG, relative to a monomeric species.

These data also indicate that the scFv2 molecules, like their CC49 IgG parent are

30 candidates for immunotherapeutic applications, but with the benefit of increased capillary
permeability and more rapid bi ©distribution pharmacokinetics. The advantage should allow
multiple injections of compounds of the present invention and give higher tumor:tissue ratios
in immunotherapeutic treatment regimens for cancer treatment, relative to the existing IgG
molecules.

35 Other embodiments of the invention will be apparent to those skilled in the art

from a consideration of this specification or practice of the invention disclosed herein. It is

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intended that the specification and examples be considered as exemplary only, with the true
scope and spirit of the invention being indicated by the following claims.

5

10

15

20

25

30

35

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WO 94/13806

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1 . A mutivalent single chain antibody which comprises two or more single
chain antibody fragments each fragment having affinity for an antigen wherein the fragments
are covalently linked by a first peptide linker and each fragment comprising:

(a) a first polypeptide comprising a light chain variable domain;
5 (b) a second polypeptide comprising a heavy chain variable domain; and

(c) a second peptide linker linking the first and second polypeptides into a
functional binding moiety.

2. The multivalent single chain antibody of Claim 1 wherein the first peptide
linker has the amino and sequence

1 o Leu Ser Ala Asp Asp Ala Lys Lys Asp Ala Ala Lys Lys Asp Asp Ala Lys Lys Asp Asp Ala Lys Lys

Asp Leu.

3. The multivalent single chain antibody of Claim 1 wherein the light chain
variable region has an amino acid sequence substantially the same as that of Figure 3 and the
heavy chain variable region has an ami no acid sequence substantially the same as that of

1 5 Figure 5.

4. The multivalent single chain antibody of Claim 1 wherein the first and
second peptide linkers have an amino acid sequence which is substantially the same.

5. A DNA sequence which codes for a mutivalent single chain antibody, the
multivalent single antibody comprising two or more single chain antibody fragments, each

20 fragment having affinity for an antigen wherein the fragments are covalently linked by a first
peptide linker and each fragment comprising:

(a) a first polypeptide comprising a light chain variable domain;

(b) a second polypeptide comprising a heavy chain variable domain; and

(c) a second peptide linker linking the first and second polypeptides into a
25 functional binding moiety.

6. The DNA sequence of Claim 5 wherein the sequence coding for the first
polypeptide is substantially the same as that of Figure 2 and the sequence coding for the
second polypeptide is substantially the same as that of Figure 3.

30

35

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FIG. 2

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GAT

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GTG

AAG

ACT

GAA

GAC

CTG

GCA

GTT

TAT

TAC

TGT

CAG

CAG

TAT

TAT

AGC

TAT

CCC

CTC

ACG

TTC

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GCT

GGG

ACC

AAG

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FIG. 3

Asp lie Val Met Ser Gin Ser Pro

Gly Glu Lys Val Thr Leu Ser Cy9

Tyr Ser Gly Asn Gin Lys Asn Tyr

Pro Gly Gin Ser Pro Lys Leu Leu

Glu Ser Gly Val Pro Asp Arg Phe

Asp Phe Thr Leu Ser lie Ser Ser

Val Tyr Tyr Cys Gin Gin Tyr Tyr

Ala Gly Thr Lys Leu Val Leu Lys

Ser

Ser

Leu

Pro

Val

Ser

Val

Lys

Ser

Ser

Gin

Ser

Leu

Leu

Leu

Ala

Trp Tyr

Gin

Gin

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He

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Ser

Tyr

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Leu

Thr

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2/20

SUBSTITUTE SHEET (RULE 26)

WO 94/13806

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FIG. 4

GAG

GTT

CAG

TTG

CAG

CAG

TCT

GGG

GCT

TCA

GTG

AAG

ATT

TCC

TTC

ACT

GAC

CAT

GCA

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CAC

CAG

GGC

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GAA

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ATT

GGA

GAT

TTT

AAA

TAC

AAT

GAG

AGG

ACT

GCA

GAC

AAA

TCC

TCC

AGC

AGC

CTG

ACA

TCT

GAG

GAT

TCT

TCC

CTG

AAT

ATG

GCC

TAC

TGG

GTC

TCC

TCA

GAC GCT GAG TTG GTG AAA CCT

TGC AAG GCT TCT GGC TAC ACC

TGG GTG AAA CAG AAC CCT GAA

TAT TTT TCT CCC GGA AAT GAT

TTC AAG GGC AAG GCC ACA CTG

ACT GCC TAC GTG CAG CTC AAC

GCA GTG TAT TTC TGT ACA AGA

GGT CAA GGA ACC TCA GTC ACC

Glu

Val

Gin

Leu

Gin

Ala

Ser

Val

Lys

He

Asp

Bis

Ala

He

His

Glu

Trp

He

Gly

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Glu

Arg

Phe

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Ser

Ser

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FIG. 5

Gin Ser Asp Ala Glu
Ser Cys Lys Ala Ser
Trp Val Lys Gin Asn
Phe Ser Pro Gly Asn
Gly Lys Ala Thr Leu
Val Gin Leu Asn Ser
Cys Thr Arg Ser Leu
Val Thr Val Ser Ser

Leu Val Lys Pro Gly

Gly Tyr Thr Phe Thr

Pro Glu Gin Gly Leu

Asp Asp Phe Lys Tyr

Thr Ala Asp Lys Ser

Leu Thr Ser Glu Asp

A9n Met Ala Tyr Trp

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SUBSTITUTE SHEET (RULE 26)

INTERNATIONAL SEARCH REPORT

Intern al Application No

PCT/US 93/12039

A. CLASSIFICATION OF SUBJECT MATTER

IPC 5 C12N15/13 C07K15/28 C12N15/62 A61K39/395

According to International Patent Classification (IPC) or to both national classification and IPC

B. FIELDS SEARCHED

Minimum documentation searched (classification system followed by classification symbols)

IPC 5 C12N C07K

Documentation searched other than minimum documentation to the extent that such documents are included in the fields searched

Electronic data base consulted during the international search (name of data base and, where practical, search terms used)

C. DOCUMENTS CONSIDERED TO BE RELEVANT

Category *

Citation of document, with indication, where appropriate, of the relevant passages

Relevant to claim No.

x

Y
Y

WO, A, 91 19739 (CELLTECH LIMITED) 26
December 1991
see example 1

CANCER RESEARCH

vol. 52, no. 12 , 15 June 1992 ,
PHILADELPHIA, PA, USA
pages 3402 - 3408

T.YOKATA ET AL. 'Rapid tumour penetration
of a single-chain Fv and comparison with
other immunoglobulin forms'
see page 3403, column 1, paragraph 4

-/—

1,5
2-4,6

3,6

LI

Further documents are listed in the continuation of box C.

m

Patent family members are listed in annex.

* Special categories of cited documents :

"A" document denning the general state of the art which is not
considered to be of particular relevance

"E* earlier document but published on or after the international
filing date

"L" document which may throw doubts on priority claim(s) or
which is cited to establish the publication date of another
citation or other special reason (as specified)

'O* document referring to an oral disclosure, use, exhibition or
other means

"P' document published prior to the international filing date but
later than the priority date claimed

*T" later document published after the international filing date
or priority date and not in conflict with the application but
cited to understand the principle or theory underlying the
invention

"X" document of particular relevance; the claimed invention
cannot be considered novel or cannot be considered to
involve an inventive step when the document is taken alone

" Y " document of particular relevance; the claimed invention
cannot be considered to involve an inventive step when the
document is combined with one or more other such docu-
ments, such combination being obvious to a person skilled
in the art.

"&" document member of the same patent family

Date of the actual completion of the international search

25 March 1994

Date of mailing of the international search report

2 7 -GV 199A

Name and mailing address of the ISA

European Patent Office, P.B. 581 8 Patent] aan 2
NL - 2280 HV Rijswijk
Tel. ( + 31-70) 340-2040, Tx. 31 651 eponl,
Fax: (+31-70) 340-3016

Authorized officer

Cupido, M

Form PCT/1SA/2I0 (second sheet) (July 1992)

page 1 of 2

INTERNATIONAL SEARCH REPORT

Intern U Application No

PCT/US 93/12039

C^Continuataon) DOCUMENTS CONSIDERED TO BE RELEVANT

Category

Citation of document, with indication, where appropriate, of the relevant passages

Relevant to claim No.

BIOCHEMISTRY

vol. 30, no. 42 , 22 October 1991 ,

EASTON, PA US

pages 10117 - 10125

M.W.PANTOLIANO ET AL. 'Conformational

stability, folding and ligand-binding

affinity of single-chain Fv immunoglobulin

fragments expressed in Escherichia coli 1

cited in the application

see page 10120, column 1, paragraph 2

EP,A,0 506 124 (TANOX BIOSYSTEMS, INC.) 30
September 1992
see example 4

W0,A,93 11161 (ENZ0N, INC.) 10 June 1993
see figure 19A

2,4

1,5

1,3-6

Form PCT/ISA/210 (continuition of second theet) (July 1992)

page 2 of 2

INTERNATIONAL SEARCH REPORT

imormation on patent family members

Intern U Application No

PCT/US 93/12039

Patent document
cited in search report

Publication
date

Patent family
member(s)

Publication
date

WO-A-91 19739

26-12-91

AU-A-
EP-A-

GB-A-
JP-T-

7983191
0486652

r2250995
5502039

07-01-92
27-05-92
24-06-92
15-04-93

EP-A-0506124

30-09-92

AU-B-
AU-A-
JP-A-

640863
1299292
5117164

02-09-93
15-10-92
14-05-93

WO-A-93 11161

10-06-93

AU-A-

3178993

28-06-93

Form PCT/ISA/210 (patent family annex) (July 1992)